HEADER HYDROLASE 30-AUG-18 5QDX
TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF PTP1B IN
TITLE 2 COMPLEX WITH COMPOUND_FMOPL000484A
CAVEAT 5QDX SEVERAL RESIDUES ARE NOT PROPERLY LINKED WITH SHORT C-N BOND
CAVEAT 2 5QDX DISTANCE FOR CERTAIN CONFORMERS.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC DOMAIN;
COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B;
COMPND 6 EC: 3.1.3.48;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PTPN1, PTP1B;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24B
KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, PROTEIN TYROSINE
KEYWDS 2 PHOSPHATASE, PTP, PROTEIN TYROSINE PHOSPHATASE 1B, PTP1B, ENZYME,
KEYWDS 3 ALLOSTERY, MULTICONFORMER, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.A.KEEDY,Z.B.HILL,J.T.BIEL,E.KANG,T.J.RETTENMAIER,J.BRANDAO-NETO,
AUTHOR 2 F.VON DELFT,J.A.WELLS,J.S.FRASER
REVDAT 3 06-MAR-24 5QDX 1 REMARK
REVDAT 2 06-FEB-19 5QDX 1 COMPND JRNL
REVDAT 1 10-OCT-18 5QDX 0
JRNL AUTH D.A.KEEDY,Z.B.HILL,J.T.BIEL,E.KANG,T.J.RETTENMAIER,
JRNL AUTH 2 J.BRANDAO-NETO,N.M.PEARCE,F.VON DELFT,J.A.WELLS,J.S.FRASER
JRNL TITL AN EXPANDED ALLOSTERIC NETWORK IN PTP1B BY MULTITEMPERATURE
JRNL TITL 2 CRYSTALLOGRAPHY, FRAGMENT SCREENING, AND COVALENT TETHERING.
JRNL REF ELIFE V. 7 2018
JRNL REFN ESSN 2050-084X
JRNL PMID 29877794
JRNL DOI 10.7554/ELIFE.36307
REMARK 2
REMARK 2 RESOLUTION. 2.06 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10.1_2155
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) : 2.06
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.00
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6
REMARK 3 NUMBER OF REFLECTIONS : 29444
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.239
REMARK 3 R VALUE (WORKING SET) : 0.238
REMARK 3 FREE R VALUE : 0.273
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.920
REMARK 3 FREE R VALUE TEST SET COUNT : 1154
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 44.0071 - 4.1221 1.00 3955 159 0.1919 0.2518
REMARK 3 2 4.1221 - 3.2721 1.00 3802 154 0.2001 0.2474
REMARK 3 3 3.2721 - 2.8586 1.00 3786 156 0.2131 0.2438
REMARK 3 4 2.8586 - 2.5973 1.00 3733 154 0.2196 0.2454
REMARK 3 5 2.5973 - 2.4111 1.00 3750 149 0.2150 0.2345
REMARK 3 6 2.4111 - 2.2690 0.86 3213 137 0.3728 0.3920
REMARK 3 7 2.2690 - 2.1554 0.85 3183 127 0.3764 0.3789
REMARK 3 8 2.1554 - 2.0615 0.77 2868 118 0.5252 0.4679
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.20
REMARK 3 SHRINKAGE RADIUS : 1.10
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.240
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 20.59
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90
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 : 0.025 9006
REMARK 3 ANGLE : 2.274 12215
REMARK 3 CHIRALITY : 0.203 1276
REMARK 3 PLANARITY : 0.014 1606
REMARK 3 DIHEDRAL : 19.137 3493
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 5QDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-18.
REMARK 100 THE DEPOSITION ID IS D_1001401826.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-SEP-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57669
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060
REMARK 200 RESOLUTION RANGE LOW (A) : 63.016
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.16200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 1.44700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.260
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 (%): 63.32
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 0.3 M MAGNESIUM
REMARK 280 ACETATE, 0.1 M HEPES PH 7.5, 0.1% BETA-MERCAPTOETHANOL, 13-14%
REMARK 280 PEG 8000, 2% ETHANOL, VAPOR DIFFUSION, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.48167
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.96333
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 70.96333
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.48167
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13630 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL
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 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 GLY A 283
REMARK 465 ASP A 284
REMARK 465 SER A 285
REMARK 465 SER A 286
REMARK 465 VAL A 287
REMARK 465 GLN A 288
REMARK 465 ASP A 289
REMARK 465 GLN A 290
REMARK 465 TRP A 291
REMARK 465 LYS A 292
REMARK 465 GLU A 293
REMARK 465 LEU A 294
REMARK 465 SER A 295
REMARK 465 HIS A 296
REMARK 465 GLU A 297
REMARK 465 ASP A 298
REMARK 465 LEU A 299
REMARK 465 GLU A 300
REMARK 465 PRO A 301
REMARK 465 PRO A 302
REMARK 465 PRO A 303
REMARK 465 GLU A 304
REMARK 465 HIS A 305
REMARK 465 ILE A 306
REMARK 465 PRO A 307
REMARK 465 PRO A 308
REMARK 465 PRO A 309
REMARK 465 PRO A 310
REMARK 465 ARG A 311
REMARK 465 PRO A 312
REMARK 465 PRO A 313
REMARK 465 LYS A 314
REMARK 465 ARG A 315
REMARK 465 ILE A 316
REMARK 465 LEU A 317
REMARK 465 GLU A 318
REMARK 465 PRO A 319
REMARK 465 HIS A 320
REMARK 465 ASN A 321
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 HE21 GLN A 61 O HOH A 501 0.49
REMARK 500 HE21 GLN A 61 O HOH A 501 0.49
REMARK 500 NE2 GLN A 61 O HOH A 501 1.14
REMARK 500 NE2 GLN A 61 O HOH A 501 1.14
REMARK 500 HE ARG A 112 O HOH A 521 1.38
REMARK 500 HE ARG A 112 O HOH A 521 1.38
REMARK 500 HG1 THR A 164 O HOH A 505 1.38
REMARK 500 HG1 THR A 164 O HOH A 505 1.38
REMARK 500 HG SER A 80 O HOH A 517 1.42
REMARK 500 HG SER A 80 O HOH A 517 1.42
REMARK 500 O1 TRS A 402 O HOH A 502 1.49
REMARK 500 H ASP A 240 O HOH A 527 1.51
REMARK 500 H ASP A 240 O HOH A 527 1.51
REMARK 500 H ASP A 240 O HOH A 527 1.52
REMARK 500 H ASP A 240 O HOH A 527 1.52
REMARK 500 HE ARG A 112 O HOH A 521 1.52
REMARK 500 HE ARG A 112 O HOH A 521 1.52
REMARK 500 OD1 ASN A 193 O HOH A 503 1.55
REMARK 500 OD1 ASN A 193 O HOH A 503 1.55
REMARK 500 OE1 GLU A 252 HZ1 LYS A 255 1.59
REMARK 500 OE1 GLU A 252 HZ1 LYS A 255 1.59
REMARK 500 OE2 GLU A 62 O HOH A 504 1.72
REMARK 500 OE2 GLU A 62 O HOH A 504 1.72
REMARK 500 OG1 THR A 164 O HOH A 505 1.82
REMARK 500 OG1 THR A 164 O HOH A 505 1.82
REMARK 500 O HOH A 652 O HOH A 682 1.88
REMARK 500 OE2 GLU A 200 O HOH A 506 1.96
REMARK 500 OE2 GLU A 200 O HOH A 506 1.96
REMARK 500 OD1 ASN A 90 O HOH A 507 1.96
REMARK 500 OD1 ASN A 90 O HOH A 507 1.96
REMARK 500 OG SER A 242 O HOH A 508 1.98
REMARK 500 OG SER A 242 O HOH A 508 1.98
REMARK 500 O HOH A 662 O HOH A 706 1.98
REMARK 500 OD1 ASN A 90 O HOH A 507 2.09
REMARK 500 O HOH A 529 O HOH A 642 2.10
REMARK 500 O SER A 187 O HOH A 509 2.11
REMARK 500 O SER A 187 O HOH A 509 2.11
REMARK 500 OD2 ASP A 63 O HOH A 510 2.11
REMARK 500 OD2 ASP A 63 O HOH A 510 2.11
REMARK 500 O HOH A 517 O HOH A 691 2.11
REMARK 500 O LYS A 41 O HOH A 511 2.13
REMARK 500 O LYS A 41 O HOH A 511 2.13
REMARK 500 OE2 GLU A 161 O HOH A 512 2.13
REMARK 500 OE2 GLU A 161 O HOH A 512 2.13
REMARK 500 N SER A 187 O HOH A 513 2.13
REMARK 500 N SER A 187 O HOH A 513 2.13
REMARK 500 OE2 GLU A 161 O HOH A 512 2.14
REMARK 500 OE2 GLU A 161 O HOH A 512 2.14
REMARK 500 O HOH A 501 O HOH A 526 2.14
REMARK 500 O HOH A 605 O HOH A 700 2.15
REMARK 500
REMARK 500 THIS ENTRY HAS 59 CLOSE CONTACTS
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 O HOH A 623 O HOH A 674 4455 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 LYS A 39 C ASN A 40 N 0.172
REMARK 500 LYS A 39 C ASN A 40 N 0.172
REMARK 500 LYS A 73 C MET A 74 N 0.212
REMARK 500 LYS A 73 C MET A 74 N 0.212
REMARK 500 GLU A 76 CD GLU A 76 OE1 -0.069
REMARK 500 GLU A 76 CD GLU A 76 OE1 -0.069
REMARK 500 VAL A 92 C GLY A 93 N -0.142
REMARK 500 VAL A 92 C GLY A 93 N -0.142
REMARK 500 GLY A 117 C GLY A 117 O -0.098
REMARK 500 GLY A 117 C GLY A 117 O -0.098
REMARK 500 GLU A 129 CD GLU A 129 OE1 -0.080
REMARK 500 GLU A 129 CD GLU A 129 OE1 -0.080
REMARK 500 GLU A 129 CD GLU A 129 OE2 -0.069
REMARK 500 GLU A 129 CD GLU A 129 OE2 -0.069
REMARK 500 TRP A 179 CB TRP A 179 CG -0.246
REMARK 500 TRP A 179 CB TRP A 179 CG -0.246
REMARK 500 ASP A 181 C PHE A 182 N -0.176
REMARK 500 ASP A 181 C PHE A 182 N -0.176
REMARK 500 SER A 205 CB SER A 205 OG -0.102
REMARK 500 SER A 205 CB SER A 205 OG -0.102
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 LEU A 37 CA - CB - CG ANGL. DEV. = 13.9 DEGREES
REMARK 500 LEU A 37 CA - CB - CG ANGL. DEV. = 13.9 DEGREES
REMARK 500 PRO A 38 C - N - CD ANGL. DEV. = -17.0 DEGREES
REMARK 500 PRO A 38 C - N - CD ANGL. DEV. = -17.0 DEGREES
REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 CYS A 121 N - CA - CB ANGL. DEV. = 9.1 DEGREES
REMARK 500 CYS A 121 N - CA - CB ANGL. DEV. = 9.1 DEGREES
REMARK 500 CYS A 121 CA - CB - SG ANGL. DEV. = 7.6 DEGREES
REMARK 500 CYS A 121 CA - CB - SG ANGL. DEV. = 7.6 DEGREES
REMARK 500 LEU A 140 CA - CB - CG ANGL. DEV. = 14.1 DEGREES
REMARK 500 LEU A 140 CA - CB - CG ANGL. DEV. = 14.1 DEGREES
REMARK 500 CYS A 226 CA - CB - SG ANGL. DEV. = 8.0 DEGREES
REMARK 500 LEU A 232 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES
REMARK 500 LEU A 232 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES
REMARK 500 LEU A 232 CB - CG - CD2 ANGL. DEV. = 11.9 DEGREES
REMARK 500 LEU A 232 CB - CG - CD2 ANGL. DEV. = 11.9 DEGREES
REMARK 500 ASP A 236 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 ASP A 236 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 ARG A 257 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES
REMARK 500 ARG A 257 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES
REMARK 500 ARG A 257 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES
REMARK 500 ARG A 257 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES
REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES
REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES
REMARK 500 GLN A 262 N - CA - C ANGL. DEV. = 18.2 DEGREES
REMARK 500 GLN A 262 N - CA - C ANGL. DEV. = 18.2 DEGREES
REMARK 500 LYS A 279 CD - CE - NZ ANGL. DEV. = 14.3 DEGREES
REMARK 500 LYS A 279 CD - CE - NZ ANGL. DEV. = 14.3 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 SER A 15 38.10 -141.09
REMARK 500 SER A 15 38.10 -141.09
REMARK 500 HIS A 60 74.86 -68.40
REMARK 500 HIS A 60 74.86 -68.40
REMARK 500 TRP A 100 -71.90 -56.98
REMARK 500 TRP A 100 -71.90 -56.98
REMARK 500 LYS A 131 71.51 -110.54
REMARK 500 LYS A 131 71.51 -110.54
REMARK 500 CYS A 215 -131.39 -129.83
REMARK 500 CYS A 215 -131.39 -129.83
REMARK 500 CYS A 215 -136.03 -140.47
REMARK 500 CYS A 215 -136.03 -140.47
REMARK 500 ILE A 219 -35.14 -134.30
REMARK 500 ILE A 219 -35.14 -134.30
REMARK 500 ILE A 261 110.95 75.35
REMARK 500 ILE A 261 110.95 75.35
REMARK 500 ILE A 261 94.96 96.55
REMARK 500 ILE A 261 94.96 96.55
REMARK 500 LYS A 279 4.08 -41.94
REMARK 500 LYS A 279 4.08 -41.94
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 GLY A 93 -10.16
REMARK 500 GLY A 93 -10.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 717 DISTANCE = 5.87 ANGSTROMS
REMARK 525 HOH A 718 DISTANCE = 5.96 ANGSTROMS
REMARK 525 HOH A 719 DISTANCE = 7.20 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue JGM A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 402
DBREF 5QDX A 1 321 UNP P18031 PTN1_HUMAN 1 321
SEQADV 5QDX SER A 32 UNP P18031 CYS 32 ENGINEERED MUTATION
SEQADV 5QDX VAL A 92 UNP P18031 CYS 92 ENGINEERED MUTATION
SEQRES 1 A 321 MET GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER
SEQRES 2 A 321 GLY SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU
SEQRES 3 A 321 ALA SER ASP PHE PRO SER ARG VAL ALA LYS LEU PRO LYS
SEQRES 4 A 321 ASN LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE
SEQRES 5 A 321 ASP HIS SER ARG ILE LYS LEU HIS GLN GLU ASP ASN ASP
SEQRES 6 A 321 TYR ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN
SEQRES 7 A 321 ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR
SEQRES 8 A 321 VAL GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER
SEQRES 9 A 321 ARG GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY
SEQRES 10 A 321 SER LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU
SEQRES 11 A 321 LYS GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR
SEQRES 12 A 321 LEU ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG
SEQRES 13 A 321 GLN LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG
SEQRES 14 A 321 GLU ILE LEU HIS PHE HIS TYR THR THR TRP PRO ASP PHE
SEQRES 15 A 321 GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU
SEQRES 16 A 321 PHE LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS
SEQRES 17 A 321 GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY ARG
SEQRES 18 A 321 SER GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU
SEQRES 19 A 321 MET ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS
SEQRES 20 A 321 LYS VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU
SEQRES 21 A 321 ILE GLN THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA
SEQRES 22 A 321 VAL ILE GLU GLY ALA LYS PHE ILE MET GLY ASP SER SER
SEQRES 23 A 321 VAL GLN ASP GLN TRP LYS GLU LEU SER HIS GLU ASP LEU
SEQRES 24 A 321 GLU PRO PRO PRO GLU HIS ILE PRO PRO PRO PRO ARG PRO
SEQRES 25 A 321 PRO LYS ARG ILE LEU GLU PRO HIS ASN
HET JGM A 401 64
HET TRS A 402 20
HETNAM JGM {N}-[(2~{S})-1-DIAZANYL-3-(4-HYDROXYPHENYL)-1-
HETNAM 2 JGM OXIDANYLIDENE-PROPAN-2-YL]ETHANAMIDE
HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
HETSYN TRS TRIS BUFFER
FORMUL 2 JGM C11 H15 N3 O3
FORMUL 3 TRS C4 H12 N O3 1+
FORMUL 4 HOH *219(H2 O)
HELIX 1 AA1 GLU A 2 GLY A 14 1 13
HELIX 2 AA2 SER A 15 ALA A 27 1 13
HELIX 3 AA3 SER A 32 LEU A 37 1 6
HELIX 4 AA4 PRO A 38 ASN A 44 5 7
HELIX 5 AA5 THR A 91 GLN A 102 1 12
HELIX 6 AA6 PRO A 188 SER A 201 1 14
HELIX 7 AA7 GLY A 220 ARG A 238 1 19
HELIX 8 AA8 ASP A 240 VAL A 244 5 5
HELIX 9 AA9 ASP A 245 ARG A 254 1 10
HELIX 10 AB1 THR A 263 MET A 282 1 20
SHEET 1 AA1 9 ARG A 56 LYS A 58 0
SHEET 2 AA1 9 TYR A 66 MET A 74 -1 O ALA A 69 N ILE A 57
SHEET 3 AA1 9 ARG A 79 THR A 84 -1 O TYR A 81 N ILE A 72
SHEET 4 AA1 9 VAL A 211 HIS A 214 1 O VAL A 211 N ILE A 82
SHEET 5 AA1 9 GLY A 106 MET A 109 1 N VAL A 108 O VAL A 212
SHEET 6 AA1 9 THR A 168 TYR A 176 1 O PHE A 174 N VAL A 107
SHEET 7 AA1 9 TYR A 153 ASN A 162 -1 N ARG A 156 O HIS A 173
SHEET 8 AA1 9 LEU A 140 ILE A 149 -1 N LYS A 141 O GLU A 161
SHEET 9 AA1 9 MET A 133 PHE A 135 -1 N PHE A 135 O LEU A 140
SHEET 1 AA2 2 MET A 114 GLU A 115 0
SHEET 2 AA2 2 SER A 118 LEU A 119 -1 O SER A 118 N GLU A 115
SITE 1 AC1 5 VAL A 184 ASP A 265 ARG A 268 PHE A 269
SITE 2 AC1 5 LEU A 272
SITE 1 AC2 5 HIS A 54 LYS A 128 GLU A 129 GLU A 130
SITE 2 AC2 5 HOH A 502
CRYST1 90.286 90.286 106.445 90.00 90.00 120.00 P 31 2 1 6
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 0.011076 0.006395 0.000000 0.00000
SCALE2 0.000000 0.012789 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009395 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
