HEADER SIGNALING PROTEIN 01-NOV-17 5YPF
TITLE P62/SQSTM1 ZZ DOMAIN WITH TRP-PEPTIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 78 KDA GLUCOSE-REGULATED PROTEIN,SEQUESTOSOME-1;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: GRP-78,ENDOPLASMIC RETICULUM LUMENAL CA(2+)-BINDING PROTEIN
COMPND 5 GRP78,HEAT SHOCK 70 KDA PROTEIN 5,IMMUNOGLOBULIN HEAVY CHAIN-BINDING
COMPND 6 PROTEIN,BIP,EBI3-ASSOCIATED PROTEIN OF 60 KDA,P60,PHOSPHOTYROSINE-
COMPND 7 INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN OF 62 KDA,UBIQUITIN-BINDING
COMPND 8 PROTEIN P62;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: HSPA5, GRP78, SQSTM1, ORCA, OSIL;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS COMPLEX, P62/SQSTM1, ZZ DOMAIN, AUTOPHAGY, N-END RULE, SIGNALING
KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR D.H.KWON,L.KIM,H.K.SONG
REVDAT 3 27-MAR-24 5YPF 1 REMARK
REVDAT 2 03-OCT-18 5YPF 1 TITLE
REVDAT 1 29-AUG-18 5YPF 0
JRNL AUTH D.H.KWON,O.H.PARK,L.KIM,Y.O.JUNG,Y.PARK,H.JEONG,J.HYUN,
JRNL AUTH 2 Y.K.KIM,H.K.SONG
JRNL TITL INSIGHTS INTO DEGRADATION MECHANISM OF N-END RULE SUBSTRATES
JRNL TITL 2 BY P62/SQSTM1 AUTOPHAGY ADAPTER.
JRNL REF NAT COMMUN V. 9 3291 2018
JRNL REFN ESSN 2041-1723
JRNL PMID 30120248
JRNL DOI 10.1038/S41467-018-05825-X
REMARK 2
REMARK 2 RESOLUTION. 2.95 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.12_2829)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.65
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 5464
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.244
REMARK 3 R VALUE (WORKING SET) : 0.240
REMARK 3 FREE R VALUE : 0.285
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.660
REMARK 3 FREE R VALUE TEST SET COUNT : 528
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 40.6497 - 4.6822 0.99 1272 141 0.2174 0.2509
REMARK 3 2 4.6822 - 3.7172 1.00 1222 130 0.2345 0.2729
REMARK 3 3 3.7172 - 3.2475 1.00 1217 129 0.2784 0.3721
REMARK 3 4 3.2475 - 2.9507 1.00 1225 128 0.2791 0.3421
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.660
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.006 1442
REMARK 3 ANGLE : 1.087 1950
REMARK 3 CHIRALITY : 0.065 208
REMARK 3 PLANARITY : 0.006 256
REMARK 3 DIHEDRAL : 13.197 850
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5YPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-17.
REMARK 100 THE DEPOSITION ID IS D_1300005678.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-AUG-16
REMARK 200 TEMPERATURE (KELVIN) : 173
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL44XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5464
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.953
REMARK 200 RESOLUTION RANGE LOW (A) : 40.650
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 10.60
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 50.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.16
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, TRIS, VAPOR DIFFUSION,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 Z,X,Y
REMARK 290 6555 Z,-X,-Y
REMARK 290 7555 -Z,-X,Y
REMARK 290 8555 -Z,X,-Y
REMARK 290 9555 Y,Z,X
REMARK 290 10555 -Y,Z,-X
REMARK 290 11555 Y,-Z,-X
REMARK 290 12555 -Y,-Z,X
REMARK 290 13555 X+1/2,Y+1/2,Z+1/2
REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290 17555 Z+1/2,X+1/2,Y+1/2
REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2
REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2
REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2
REMARK 290 21555 Y+1/2,Z+1/2,X+1/2
REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2
REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2
REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.48200
REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 57.48200
REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 57.48200
REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 57.48200
REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 57.48200
REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 57.48200
REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 57.48200
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 57.48200
REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 57.48200
REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 57.48200
REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 57.48200
REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 57.48200
REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 57.48200
REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 57.48200
REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 57.48200
REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 57.48200
REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 57.48200
REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 57.48200
REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 57.48200
REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 57.48200
REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 57.48200
REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 57.48200
REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 57.48200
REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 57.48200
REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 57.48200
REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 57.48200
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3, 4
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 4
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER A 46
REMARK 465 PRO A 47
REMARK 465 PHE A 48
REMARK 465 GLY A 49
REMARK 465 HIS A 50
REMARK 465 LEU A 51
REMARK 465 SER A 52
REMARK 465 GLU A 53
REMARK 465 GLY A 54
REMARK 465 PHE A 55
REMARK 465 SER A 56
REMARK 465 SER B 46
REMARK 465 PRO B 47
REMARK 465 PHE B 48
REMARK 465 GLY B 49
REMARK 465 HIS B 50
REMARK 465 LEU B 51
REMARK 465 SER B 52
REMARK 465 GLU B 53
REMARK 465 GLY B 54
REMARK 465 PHE B 55
REMARK 465 SER B 56
REMARK 465 TRP C -3
REMARK 465 GLU C -2
REMARK 465 GLU C -1
REMARK 465 GLU C 0
REMARK 465 SER C 46
REMARK 465 PRO C 47
REMARK 465 PHE C 48
REMARK 465 GLY C 49
REMARK 465 HIS C 50
REMARK 465 LEU C 51
REMARK 465 SER C 52
REMARK 465 GLU C 53
REMARK 465 GLY C 54
REMARK 465 PHE C 55
REMARK 465 SER C 56
REMARK 465 TRP D -3
REMARK 465 GLU D -2
REMARK 465 GLU D -1
REMARK 465 GLU D 0
REMARK 465 SER D 46
REMARK 465 PRO D 47
REMARK 465 PHE D 48
REMARK 465 GLY D 49
REMARK 465 HIS D 50
REMARK 465 LEU D 51
REMARK 465 SER D 52
REMARK 465 GLU D 53
REMARK 465 GLY D 54
REMARK 465 PHE D 55
REMARK 465 SER D 56
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 HG CYS A 7 ZN ZN A 101 1.15
REMARK 500 HG CYS D 4 ZN ZN D 101 1.22
REMARK 500 HG CYS D 18 ZN ZN D 102 1.24
REMARK 500 HD1 HIS A 39 ZN ZN A 102 1.39
REMARK 500 HG CYS A 27 ZN ZN A 101 1.42
REMARK 500 O VAL A 12 HH11 ARG B 37 1.43
REMARK 500 H ASP D 5 O ASP D 25 1.48
REMARK 500 O VAL A 12 NH1 ARG B 37 2.13
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 OG1 THR A 40 O SER D 19 17545 2.08
REMARK 500 OG1 THR B 40 O SER C 19 20746 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG B 37 NE - CZ - NH1 ANGL. DEV. = -6.9 DEGREES
REMARK 500 ARG B 37 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 VAL A 20 -61.31 -100.17
REMARK 500 VAL B 20 -61.53 -100.40
REMARK 500 ASN C 8 15.33 58.36
REMARK 500 VAL D 20 -60.70 -102.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 4 SG
REMARK 620 2 CYS A 7 SG 114.1
REMARK 620 3 CYS A 27 SG 110.7 108.7
REMARK 620 4 CYS A 30 SG 95.9 121.3 105.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 18 SG
REMARK 620 2 CYS A 21 SG 92.2
REMARK 620 3 HIS A 36 NE2 113.5 82.7
REMARK 620 4 HIS A 39 ND1 133.7 88.9 112.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 4 SG
REMARK 620 2 CYS B 7 SG 104.7
REMARK 620 3 CYS B 27 SG 117.2 116.3
REMARK 620 4 CYS B 30 SG 92.1 114.2 110.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 18 SG
REMARK 620 2 CYS B 21 SG 103.5
REMARK 620 3 HIS B 36 NE2 114.2 74.9
REMARK 620 4 HIS B 39 ND1 139.4 83.9 106.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN C 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 4 SG
REMARK 620 2 CYS C 7 SG 106.4
REMARK 620 3 CYS C 27 SG 122.5 94.5
REMARK 620 4 CYS C 30 SG 110.3 112.3 109.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN C 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 18 SG
REMARK 620 2 CYS C 21 SG 94.4
REMARK 620 3 HIS C 36 NE2 115.4 86.5
REMARK 620 4 HIS C 39 ND1 119.4 83.1 124.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN D 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS D 4 SG
REMARK 620 2 CYS D 7 SG 92.4
REMARK 620 3 CYS D 27 SG 130.0 101.6
REMARK 620 4 CYS D 30 SG 99.2 112.6 118.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN D 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS D 18 SG
REMARK 620 2 CYS D 21 SG 114.7
REMARK 620 3 HIS D 36 NE2 102.0 124.2
REMARK 620 4 HIS D 39 ND1 100.5 114.7 97.0
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 102
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 TRP (-3 POSITION) IS SYNTHETIC RESIDUE GENERATED BY SPECIAL ENZYME
DBREF 5YPF A -2 1 UNP P11021 GRP78_HUMAN 19 22
DBREF 5YPF A 2 56 UNP Q13501 SQSTM_HUMAN 126 180
DBREF 5YPF B -2 1 UNP P11021 GRP78_HUMAN 19 22
DBREF 5YPF B 2 56 UNP Q13501 SQSTM_HUMAN 126 180
DBREF 5YPF C -2 1 UNP P11021 GRP78_HUMAN 19 22
DBREF 5YPF C 2 56 UNP Q13501 SQSTM_HUMAN 126 180
DBREF 5YPF D -2 1 UNP P11021 GRP78_HUMAN 19 22
DBREF 5YPF D 2 56 UNP Q13501 SQSTM_HUMAN 126 180
SEQADV 5YPF TRP A -3 UNP P11021 SEE SEQUENCE DETAILS
SEQADV 5YPF TRP B -3 UNP P11021 SEE SEQUENCE DETAILS
SEQADV 5YPF TRP C -3 UNP P11021 SEE SEQUENCE DETAILS
SEQADV 5YPF TRP D -3 UNP P11021 SEE SEQUENCE DETAILS
SEQRES 1 A 60 TRP GLU GLU GLU ASP VAL ILE CYS ASP GLY CYS ASN GLY
SEQRES 2 A 60 PRO VAL VAL GLY THR ARG TYR LYS CYS SER VAL CYS PRO
SEQRES 3 A 60 ASP TYR ASP LEU CYS SER VAL CYS GLU GLY LYS GLY LEU
SEQRES 4 A 60 HIS ARG GLY HIS THR LYS LEU ALA PHE PRO SER PRO PHE
SEQRES 5 A 60 GLY HIS LEU SER GLU GLY PHE SER
SEQRES 1 B 60 TRP GLU GLU GLU ASP VAL ILE CYS ASP GLY CYS ASN GLY
SEQRES 2 B 60 PRO VAL VAL GLY THR ARG TYR LYS CYS SER VAL CYS PRO
SEQRES 3 B 60 ASP TYR ASP LEU CYS SER VAL CYS GLU GLY LYS GLY LEU
SEQRES 4 B 60 HIS ARG GLY HIS THR LYS LEU ALA PHE PRO SER PRO PHE
SEQRES 5 B 60 GLY HIS LEU SER GLU GLY PHE SER
SEQRES 1 C 60 TRP GLU GLU GLU ASP VAL ILE CYS ASP GLY CYS ASN GLY
SEQRES 2 C 60 PRO VAL VAL GLY THR ARG TYR LYS CYS SER VAL CYS PRO
SEQRES 3 C 60 ASP TYR ASP LEU CYS SER VAL CYS GLU GLY LYS GLY LEU
SEQRES 4 C 60 HIS ARG GLY HIS THR LYS LEU ALA PHE PRO SER PRO PHE
SEQRES 5 C 60 GLY HIS LEU SER GLU GLY PHE SER
SEQRES 1 D 60 TRP GLU GLU GLU ASP VAL ILE CYS ASP GLY CYS ASN GLY
SEQRES 2 D 60 PRO VAL VAL GLY THR ARG TYR LYS CYS SER VAL CYS PRO
SEQRES 3 D 60 ASP TYR ASP LEU CYS SER VAL CYS GLU GLY LYS GLY LEU
SEQRES 4 D 60 HIS ARG GLY HIS THR LYS LEU ALA PHE PRO SER PRO PHE
SEQRES 5 D 60 GLY HIS LEU SER GLU GLY PHE SER
HET ZN A 101 1
HET ZN A 102 1
HET ZN B 101 1
HET ZN B 102 1
HET ZN C 101 1
HET ZN C 102 1
HET ZN D 101 1
HET ZN D 102 1
HETNAM ZN ZINC ION
FORMUL 5 ZN 8(ZN 2+)
HELIX 1 AA1 CYS A 27 LYS A 33 1 7
HELIX 2 AA2 CYS B 27 LYS B 33 1 7
HELIX 3 AA3 CYS C 27 LYS C 33 1 7
HELIX 4 AA4 CYS D 27 LYS D 33 1 7
SHEET 1 AA1 3 ASP A 25 LEU A 26 0
SHEET 2 AA1 3 ARG A 15 CYS A 18 -1 N TYR A 16 O LEU A 26
SHEET 3 AA1 3 LYS A 41 PHE A 44 -1 O PHE A 44 N ARG A 15
SHEET 1 AA2 6 ASP B 25 LEU B 26 0
SHEET 2 AA2 6 ARG B 15 CYS B 18 -1 N TYR B 16 O LEU B 26
SHEET 3 AA2 6 LYS B 41 PHE B 44 -1 O LEU B 42 N LYS B 17
SHEET 4 AA2 6 LYS D 41 PHE D 44 -1 O ALA D 43 N LYS B 41
SHEET 5 AA2 6 ARG D 15 CYS D 18 -1 N LYS D 17 O LEU D 42
SHEET 6 AA2 6 ASP D 25 LEU D 26 -1 O LEU D 26 N TYR D 16
SHEET 1 AA3 3 ASP C 25 LEU C 26 0
SHEET 2 AA3 3 ARG C 15 CYS C 18 -1 N TYR C 16 O LEU C 26
SHEET 3 AA3 3 LYS C 41 PHE C 44 -1 O LEU C 42 N LYS C 17
LINK SG CYS A 4 ZN ZN A 101 1555 1555 2.27
LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.21
LINK SG CYS A 18 ZN ZN A 102 1555 1555 2.31
LINK SG CYS A 21 ZN ZN A 102 1555 1555 2.62
LINK SG CYS A 27 ZN ZN A 101 1555 1555 2.35
LINK SG CYS A 30 ZN ZN A 101 1555 1555 2.31
LINK NE2 HIS A 36 ZN ZN A 102 1555 1555 2.04
LINK ND1 HIS A 39 ZN ZN A 102 1555 1555 1.99
LINK SG CYS B 4 ZN ZN B 101 1555 1555 2.25
LINK SG CYS B 7 ZN ZN B 101 1555 1555 2.29
LINK SG CYS B 18 ZN ZN B 102 1555 1555 2.21
LINK SG CYS B 21 ZN ZN B 102 1555 1555 2.54
LINK SG CYS B 27 ZN ZN B 101 1555 1555 2.41
LINK SG CYS B 30 ZN ZN B 101 1555 1555 2.31
LINK NE2 HIS B 36 ZN ZN B 102 1555 1555 2.04
LINK ND1 HIS B 39 ZN ZN B 102 1555 1555 1.98
LINK SG CYS C 4 ZN ZN C 101 1555 1555 2.15
LINK SG CYS C 7 ZN ZN C 101 1555 1555 2.15
LINK SG CYS C 18 ZN ZN C 102 1555 1555 2.27
LINK SG CYS C 21 ZN ZN C 102 1555 1555 2.55
LINK SG CYS C 27 ZN ZN C 101 1555 1555 2.51
LINK SG CYS C 30 ZN ZN C 101 1555 1555 2.27
LINK NE2 HIS C 36 ZN ZN C 102 1555 1555 2.10
LINK ND1 HIS C 39 ZN ZN C 102 1555 1555 2.01
LINK SG CYS D 4 ZN ZN D 101 1555 1555 2.35
LINK SG CYS D 7 ZN ZN D 101 1555 1555 2.20
LINK SG CYS D 18 ZN ZN D 102 1555 1555 2.38
LINK SG CYS D 21 ZN ZN D 102 1555 1555 2.42
LINK SG CYS D 27 ZN ZN D 101 1555 1555 2.27
LINK SG CYS D 30 ZN ZN D 101 1555 1555 2.29
LINK NE2 HIS D 36 ZN ZN D 102 1555 1555 2.06
LINK ND1 HIS D 39 ZN ZN D 102 1555 1555 2.08
SITE 1 AC1 4 CYS A 4 CYS A 7 CYS A 27 CYS A 30
SITE 1 AC2 4 CYS A 18 CYS A 21 HIS A 36 HIS A 39
SITE 1 AC3 4 CYS B 4 CYS B 7 CYS B 27 CYS B 30
SITE 1 AC4 4 CYS B 18 CYS B 21 HIS B 36 HIS B 39
SITE 1 AC5 4 CYS C 4 CYS C 7 CYS C 27 CYS C 30
SITE 1 AC6 4 CYS C 18 CYS C 21 HIS C 36 HIS C 39
SITE 1 AC7 4 CYS D 4 CYS D 7 CYS D 27 CYS D 30
SITE 1 AC8 4 CYS D 18 CYS D 21 HIS D 36 HIS D 39
CRYST1 114.964 114.964 114.964 90.00 90.00 90.00 I 2 3 96
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.008698 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008698 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008698 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
