HEADER TRANSFERASE 16-MAR-17 5NG0
TITLE STRUCTURE OF RIP2K(L294F) WITH BOUND AMPPCP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME-
COMPND 5 ASSOCIATED KINASE,CARD-CONTAINING IL-1 BETA ICE-KINASE,RIP-LIKE-
COMPND 6 INTERACTING CLARP KINASE,RECEPTOR-INTERACTING PROTEIN 2,RIP-2,
COMPND 7 TYROSINE-PROTEIN KINASE RIPK2;
COMPND 8 EC: 2.7.11.1,2.7.10.2;
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: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108
KEYWDS RIP2K, KINASE, ACTIVE STATE, AMPPCPP, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.PELLEGRINI,S.CUSACK
REVDAT 4 17-JAN-24 5NG0 1 LINK
REVDAT 3 16-OCT-19 5NG0 1 REMARK
REVDAT 2 06-DEC-17 5NG0 1 JRNL
REVDAT 1 07-JUN-17 5NG0 0
JRNL AUTH E.PELLEGRINI,L.SIGNOR,S.SINGH,E.BOERI ERBA,S.CUSACK
JRNL TITL STRUCTURES OF THE INACTIVE AND ACTIVE STATES OF RIP2 KINASE
JRNL TITL 2 INFORM ON THE MECHANISM OF ACTIVATION.
JRNL REF PLOS ONE V. 12 77161 2017
JRNL REFN ESSN 1932-6203
JRNL PMID 28545134
JRNL DOI 10.1371/JOURNAL.PONE.0177161
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0158
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8
REMARK 3 NUMBER OF REFLECTIONS : 54007
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.171
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : 0.191
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2886
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2988
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.50
REMARK 3 BIN R VALUE (WORKING SET) : 0.2370
REMARK 3 BIN FREE R VALUE SET COUNT : 162
REMARK 3 BIN FREE R VALUE : 0.2550
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4481
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 65
REMARK 3 SOLVENT ATOMS : 397
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.92
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.40000
REMARK 3 B22 (A**2) : 1.40000
REMARK 3 B33 (A**2) : -2.79000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.137
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.977
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4740 ; 0.040 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6463 ; 1.338 ; 1.976
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 566 ; 5.653 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 216 ;34.604 ;23.333
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 770 ;13.517 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.704 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 709 ; 0.090 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3588 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2240 ; 2.192 ; 3.643
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2796 ; 3.491 ; 5.435
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2500 ; 2.878 ; 3.838
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7243 ; 6.926 ;48.734
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NCS TYPE: LOCAL
REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1
REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT
REMARK 3 1 A 6 299 B 6 299 18120 0.07 0.05
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN
REMARK 3 THE INPUT
REMARK 4
REMARK 4 5NG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-17.
REMARK 100 THE DEPOSITION ID IS D_1200004061.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-NOV-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.976
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54007
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 47.250
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.03500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.9000
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: 2FB8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 61.58
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES 100 MM PH 7.5, 1 MM MGCL2, 2.0 M
REMARK 280 LICL AND 5% PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+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 100.62500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.09000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.09000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.31250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.09000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.09000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 150.93750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.09000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.09000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.31250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.09000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.09000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 150.93750
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 100.62500
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4960 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25200 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 -3
REMARK 465 ALA A -2
REMARK 465 MET A -1
REMARK 465 ALA A 0
REMARK 465 MET A 1
REMARK 465 ASN A 2
REMARK 465 GLY A 3
REMARK 465 GLU A 4
REMARK 465 ALA A 5
REMARK 465 MET A 173
REMARK 465 SER A 174
REMARK 465 LEU A 175
REMARK 465 SER A 176
REMARK 465 GLN A 177
REMARK 465 SER A 178
REMARK 465 ARG A 179
REMARK 465 SER A 180
REMARK 465 SER A 181
REMARK 465 LYS A 182
REMARK 465 SER A 183
REMARK 465 ALA A 184
REMARK 465 PRO A 185
REMARK 465 GLU A 186
REMARK 465 GLY A 187
REMARK 465 GLY A 201
REMARK 465 GLN A 202
REMARK 465 LYS A 203
REMARK 465 SER A 204
REMARK 465 ARG A 205
REMARK 465 ALA A 206
REMARK 465 GLY B -3
REMARK 465 ALA B -2
REMARK 465 MET B -1
REMARK 465 ALA B 0
REMARK 465 MET B 1
REMARK 465 ASN B 2
REMARK 465 GLY B 3
REMARK 465 GLU B 4
REMARK 465 MET B 173
REMARK 465 SER B 174
REMARK 465 LEU B 175
REMARK 465 SER B 176
REMARK 465 GLN B 177
REMARK 465 SER B 178
REMARK 465 ARG B 179
REMARK 465 SER B 180
REMARK 465 SER B 181
REMARK 465 LYS B 182
REMARK 465 GLN B 202
REMARK 465 LYS B 203
REMARK 465 SER B 204
REMARK 465 ILE B 300
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 26 CG CD NE CZ NH1 NH2
REMARK 470 HIS A 52 CG ND1 CD2 CE1 NE2
REMARK 470 THR A 53 OG1 CG2
REMARK 470 LEU A 56 CG CD1 CD2
REMARK 470 GLU A 298 CG CD OE1 OE2
REMARK 470 GLU A 299 CG CD OE1 OE2
REMARK 470 ARG B 26 CG CD NE CZ NH1 NH2
REMARK 470 ILE B 51 CG1 CG2 CD1
REMARK 470 HIS B 52 CG ND1 CD2 CE1 NE2
REMARK 470 LEU B 56 CG CD1 CD2
REMARK 470 ARG B 205 CG CD NE CZ NH1 NH2
REMARK 470 GLU B 230 CG CD OE1 OE2
REMARK 470 GLU B 298 CG CD OE1 OE2
REMARK 470 GLU B 299 CG CD OE1 OE2
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 O HOH B 676 O HOH B 684 2.03
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 ASP A 146 38.01 -143.84
REMARK 500 ASP A 155 -167.69 -79.84
REMARK 500 ASP A 164 77.58 62.78
REMARK 500 ASP B 146 39.27 -142.65
REMARK 500 ASP B 155 -168.17 -78.42
REMARK 500 ASP B 164 77.78 62.29
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 MG A1001 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 164 OD1
REMARK 620 2 ASP A 164 OD2 59.7
REMARK 620 3 ACP A1000 O1G 155.0 99.2
REMARK 620 4 ACP A1000 O1B 86.0 85.6 78.7
REMARK 620 5 HOH A1153 O 76.4 90.2 119.7 161.5
REMARK 620 6 HOH A1259 O 98.7 158.4 101.9 93.8 83.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG B 402 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 164 OD1
REMARK 620 2 ASP B 164 OD2 60.9
REMARK 620 3 ACP B 401 O2G 158.6 99.2
REMARK 620 4 ACP B 401 O2B 83.3 86.0 87.8
REMARK 620 5 HOH B 511 O 81.1 87.0 107.1 164.4
REMARK 620 6 HOH B 647 O 92.4 152.8 108.0 96.5 83.6
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACP A 1000
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACP B 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402
DBREF 5NG0 A 1 300 UNP O43353 RIPK2_HUMAN 1 300
DBREF 5NG0 B 1 300 UNP O43353 RIPK2_HUMAN 1 300
SEQADV 5NG0 GLY A -3 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 ALA A -2 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 MET A -1 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 ALA A 0 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 PHE A 294 UNP O43353 LEU 294 ENGINEERED MUTATION
SEQADV 5NG0 GLY B -3 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 ALA B -2 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 MET B -1 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 ALA B 0 UNP O43353 EXPRESSION TAG
SEQADV 5NG0 PHE B 294 UNP O43353 LEU 294 ENGINEERED MUTATION
SEQRES 1 A 304 GLY ALA MET ALA MET ASN GLY GLU ALA ILE CYS SER ALA
SEQRES 2 A 304 LEU PRO THR ILE PRO TYR HIS LYS LEU ALA ASP LEU ARG
SEQRES 3 A 304 TYR LEU SER ARG GLY ALA SER GLY THR VAL SER SER ALA
SEQRES 4 A 304 ARG HIS ALA ASP TRP ARG VAL GLN VAL ALA VAL LYS HIS
SEQRES 5 A 304 LEU HIS ILE HIS THR PRO LEU LEU ASP SER GLU ARG LYS
SEQRES 6 A 304 ASP VAL LEU ARG GLU ALA GLU ILE LEU HIS LYS ALA ARG
SEQRES 7 A 304 PHE SER TYR ILE LEU PRO ILE LEU GLY ILE CYS ASN GLU
SEQRES 8 A 304 PRO GLU PHE LEU GLY ILE VAL THR GLU TYR MET PRO ASN
SEQRES 9 A 304 GLY SER LEU ASN GLU LEU LEU HIS ARG LYS THR GLU TYR
SEQRES 10 A 304 PRO ASP VAL ALA TRP PRO LEU ARG PHE ARG ILE LEU HIS
SEQRES 11 A 304 GLU ILE ALA LEU GLY VAL ASN TYR LEU HIS ASN MET THR
SEQRES 12 A 304 PRO PRO LEU LEU HIS HIS ASP LEU LYS THR GLN ASN ILE
SEQRES 13 A 304 LEU LEU ASP ASN GLU PHE HIS VAL LYS ILE ALA ASP PHE
SEQRES 14 A 304 GLY LEU SER LYS TRP ARG MET MET SER LEU SER GLN SER
SEQRES 15 A 304 ARG SER SER LYS SER ALA PRO GLU GLY GLY THR ILE ILE
SEQRES 16 A 304 TYR MET PRO PRO GLU ASN TYR GLU PRO GLY GLN LYS SER
SEQRES 17 A 304 ARG ALA SER ILE LYS HIS ASP ILE TYR SER TYR ALA VAL
SEQRES 18 A 304 ILE THR TRP GLU VAL LEU SER ARG LYS GLN PRO PHE GLU
SEQRES 19 A 304 ASP VAL THR ASN PRO LEU GLN ILE MET TYR SER VAL SER
SEQRES 20 A 304 GLN GLY HIS ARG PRO VAL ILE ASN GLU GLU SER LEU PRO
SEQRES 21 A 304 TYR ASP ILE PRO HIS ARG ALA ARG MET ILE SER LEU ILE
SEQRES 22 A 304 GLU SER GLY TRP ALA GLN ASN PRO ASP GLU ARG PRO SER
SEQRES 23 A 304 PHE LEU LYS CYS LEU ILE GLU LEU GLU PRO VAL PHE ARG
SEQRES 24 A 304 THR PHE GLU GLU ILE
SEQRES 1 B 304 GLY ALA MET ALA MET ASN GLY GLU ALA ILE CYS SER ALA
SEQRES 2 B 304 LEU PRO THR ILE PRO TYR HIS LYS LEU ALA ASP LEU ARG
SEQRES 3 B 304 TYR LEU SER ARG GLY ALA SER GLY THR VAL SER SER ALA
SEQRES 4 B 304 ARG HIS ALA ASP TRP ARG VAL GLN VAL ALA VAL LYS HIS
SEQRES 5 B 304 LEU HIS ILE HIS THR PRO LEU LEU ASP SER GLU ARG LYS
SEQRES 6 B 304 ASP VAL LEU ARG GLU ALA GLU ILE LEU HIS LYS ALA ARG
SEQRES 7 B 304 PHE SER TYR ILE LEU PRO ILE LEU GLY ILE CYS ASN GLU
SEQRES 8 B 304 PRO GLU PHE LEU GLY ILE VAL THR GLU TYR MET PRO ASN
SEQRES 9 B 304 GLY SER LEU ASN GLU LEU LEU HIS ARG LYS THR GLU TYR
SEQRES 10 B 304 PRO ASP VAL ALA TRP PRO LEU ARG PHE ARG ILE LEU HIS
SEQRES 11 B 304 GLU ILE ALA LEU GLY VAL ASN TYR LEU HIS ASN MET THR
SEQRES 12 B 304 PRO PRO LEU LEU HIS HIS ASP LEU LYS THR GLN ASN ILE
SEQRES 13 B 304 LEU LEU ASP ASN GLU PHE HIS VAL LYS ILE ALA ASP PHE
SEQRES 14 B 304 GLY LEU SER LYS TRP ARG MET MET SER LEU SER GLN SER
SEQRES 15 B 304 ARG SER SER LYS SER ALA PRO GLU GLY GLY THR ILE ILE
SEQRES 16 B 304 TYR MET PRO PRO GLU ASN TYR GLU PRO GLY GLN LYS SER
SEQRES 17 B 304 ARG ALA SER ILE LYS HIS ASP ILE TYR SER TYR ALA VAL
SEQRES 18 B 304 ILE THR TRP GLU VAL LEU SER ARG LYS GLN PRO PHE GLU
SEQRES 19 B 304 ASP VAL THR ASN PRO LEU GLN ILE MET TYR SER VAL SER
SEQRES 20 B 304 GLN GLY HIS ARG PRO VAL ILE ASN GLU GLU SER LEU PRO
SEQRES 21 B 304 TYR ASP ILE PRO HIS ARG ALA ARG MET ILE SER LEU ILE
SEQRES 22 B 304 GLU SER GLY TRP ALA GLN ASN PRO ASP GLU ARG PRO SER
SEQRES 23 B 304 PHE LEU LYS CYS LEU ILE GLU LEU GLU PRO VAL PHE ARG
SEQRES 24 B 304 THR PHE GLU GLU ILE
HET ACP A1000 31
HET MG A1001 1
HET ACP B 401 31
HET MG B 402 1
HET CO B 403 1
HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
HETNAM MG MAGNESIUM ION
HETNAM CO COBALT (II) ION
HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
FORMUL 3 ACP 2(C11 H18 N5 O12 P3)
FORMUL 4 MG 2(MG 2+)
FORMUL 7 CO CO 2+
FORMUL 8 HOH *397(H2 O)
HELIX 1 AA1 PRO A 14 HIS A 16 5 3
HELIX 2 AA2 LEU A 56 ALA A 73 1 18
HELIX 3 AA3 SER A 102 ARG A 109 1 8
HELIX 4 AA4 ALA A 117 ASN A 137 1 21
HELIX 5 AA5 LYS A 148 GLN A 150 5 3
HELIX 6 AA6 PRO A 194 TYR A 198 5 5
HELIX 7 AA7 LYS A 209 ARG A 225 1 17
HELIX 8 AA8 ASN A 234 GLN A 244 1 11
HELIX 9 AA9 HIS A 261 TRP A 273 1 13
HELIX 10 AB1 ASN A 276 ARG A 280 5 5
HELIX 11 AB2 SER A 282 THR A 296 1 15
HELIX 12 AB3 PRO B 14 HIS B 16 5 3
HELIX 13 AB4 LEU B 56 ALA B 73 1 18
HELIX 14 AB5 SER B 102 ARG B 109 1 8
HELIX 15 AB6 ALA B 117 ASN B 137 1 21
HELIX 16 AB7 LYS B 148 GLN B 150 5 3
HELIX 17 AB8 THR B 189 MET B 193 5 5
HELIX 18 AB9 PRO B 194 TYR B 198 5 5
HELIX 19 AC1 ARG B 205 ILE B 208 5 4
HELIX 20 AC2 LYS B 209 ARG B 225 1 17
HELIX 21 AC3 ASN B 234 GLN B 244 1 11
HELIX 22 AC4 HIS B 261 TRP B 273 1 13
HELIX 23 AC5 ASN B 276 ARG B 280 5 5
HELIX 24 AC6 SER B 282 THR B 296 1 15
SHEET 1 AA1 2 CYS A 7 ALA A 9 0
SHEET 2 AA1 2 CYS B 7 ALA B 9 -1 O SER B 8 N SER A 8
SHEET 1 AA2 5 LEU A 18 ARG A 26 0
SHEET 2 AA2 5 THR A 31 HIS A 37 -1 O VAL A 32 N SER A 25
SHEET 3 AA2 5 GLN A 43 HIS A 48 -1 O VAL A 46 N SER A 33
SHEET 4 AA2 5 PHE A 90 GLU A 96 -1 O ILE A 93 N LYS A 47
SHEET 5 AA2 5 ILE A 81 GLU A 87 -1 N GLU A 87 O PHE A 90
SHEET 1 AA3 2 LEU A 142 LEU A 143 0
SHEET 2 AA3 2 LYS A 169 TRP A 170 -1 O LYS A 169 N LEU A 143
SHEET 1 AA4 2 ILE A 152 LEU A 154 0
SHEET 2 AA4 2 VAL A 160 ILE A 162 -1 O LYS A 161 N LEU A 153
SHEET 1 AA5 5 LEU B 18 ARG B 26 0
SHEET 2 AA5 5 THR B 31 HIS B 37 -1 O VAL B 32 N SER B 25
SHEET 3 AA5 5 GLN B 43 HIS B 48 -1 O VAL B 46 N SER B 33
SHEET 4 AA5 5 PHE B 90 GLU B 96 -1 O THR B 95 N ALA B 45
SHEET 5 AA5 5 ILE B 81 GLU B 87 -1 N GLU B 87 O PHE B 90
SHEET 1 AA6 2 LEU B 142 LEU B 143 0
SHEET 2 AA6 2 LYS B 169 TRP B 170 -1 O LYS B 169 N LEU B 143
SHEET 1 AA7 2 ILE B 152 LEU B 154 0
SHEET 2 AA7 2 VAL B 160 ILE B 162 -1 O LYS B 161 N LEU B 153
SSBOND 1 CYS A 7 CYS B 7 1555 1555 2.05
LINK OD1 ASP A 164 MG MG A1001 1555 1555 2.20
LINK OD2 ASP A 164 MG MG A1001 1555 1555 2.18
LINK O1G ACP A1000 MG MG A1001 1555 1555 2.18
LINK O1B ACP A1000 MG MG A1001 1555 1555 2.18
LINK MG MG A1001 O HOH A1153 1555 1555 2.20
LINK MG MG A1001 O HOH A1259 1555 1555 2.17
LINK OD1 ASP B 164 MG MG B 402 1555 1555 2.19
LINK OD2 ASP B 164 MG MG B 402 1555 1555 2.18
LINK O2G ACP B 401 MG MG B 402 1555 1555 2.16
LINK O2B ACP B 401 MG MG B 402 1555 1555 2.17
LINK MG MG B 402 O HOH B 511 1555 1555 2.19
LINK MG MG B 402 O HOH B 647 1555 1555 2.18
CISPEP 1 THR A 139 PRO A 140 0 0.57
CISPEP 2 THR B 139 PRO B 140 0 -0.43
SITE 1 AC1 19 SER A 29 VAL A 32 ALA A 45 LYS A 47
SITE 2 AC1 19 LEU A 79 THR A 95 GLU A 96 MET A 98
SITE 3 AC1 19 GLN A 150 ASN A 151 LEU A 153 ASP A 164
SITE 4 AC1 19 MG A1001 HOH A1104 HOH A1114 HOH A1141
SITE 5 AC1 19 HOH A1231 HOH A1234 HOH A1238
SITE 1 AC2 4 ASP A 164 ACP A1000 HOH A1153 HOH A1259
SITE 1 AC3 17 SER B 29 VAL B 32 ALA B 45 LYS B 47
SITE 2 AC3 17 LEU B 79 THR B 95 GLU B 96 MET B 98
SITE 3 AC3 17 GLN B 150 ASN B 151 LEU B 153 ASP B 164
SITE 4 AC3 17 MG B 402 HOH B 514 HOH B 517 HOH B 622
SITE 5 AC3 17 HOH B 625
SITE 1 AC4 4 ASP B 164 ACP B 401 HOH B 511 HOH B 647
CRYST1 94.180 94.180 201.250 90.00 90.00 90.00 P 41 21 2 16
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 0.010618 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010618 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004969 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
