HEADER HYDROLASE/INHIBITOR 15-DEC-11 3V4O
TITLE HUMAN MALT1 (CASPASE DOMAIN) IN COMPLEX WITH AN IRREVERSIBLE PEPTIDIC
TITLE 2 INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MUCOSA-ASSOCIATED LYMPHOID TISSUE LYMPHOMA TRANSLOCATION
COMPND 3 PROTEIN 1;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: UNP RESIDUES 329-569;
COMPND 6 SYNONYM: MALT LYMPHOMA-ASSOCIATED TRANSLOCATION, PARACASPASE;
COMPND 7 EC: 3.4.22.-;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: MALT1 INHIBITOR;
COMPND 11 CHAIN: B;
COMPND 12 SYNONYM: Z-VRPR-FMK;
COMPND 13 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: MALT1, MLT;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES
KEYWDS CASPASE, HYDROLASE, TRAF6, BCL10, CYTOSOLIC, HYDROLASE-INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.RENATUS,C.WIESMANN
REVDAT 5 29-NOV-23 3V4O 1 REMARK
REVDAT 4 13-SEP-23 3V4O 1 SEQADV LINK
REVDAT 3 08-NOV-17 3V4O 1 REMARK
REVDAT 2 09-MAY-12 3V4O 1 JRNL
REVDAT 1 14-MAR-12 3V4O 0
JRNL AUTH C.WIESMANN,L.LEDER,J.BLANK,A.BERNARDI,S.MELKKO,A.DECOCK,
JRNL AUTH 2 A.D'ARCY,F.VILLARD,P.ERBEL,N.HUGHES,F.FREULER,R.NIKOLAY,
JRNL AUTH 3 J.ALVES,F.BORNANCIN,M.RENATUS
JRNL TITL STRUCTURAL DETERMINANTS OF MALT1 PROTEASE ACTIVITY.
JRNL REF J.MOL.BIOL. V. 419 4 2012
JRNL REFN ISSN 0022-2836
JRNL PMID 22366302
JRNL DOI 10.1016/J.JMB.2012.02.018
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.86
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 18482
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : FREE R VALUE TEST SET SIZE
REMARK 3 (%) : 5.0
REMARK 3 R VALUE (WORKING + TEST SET) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.228
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 973
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE SET COUNT : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1910
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 150
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 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): NULL
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
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 NUMBER OF DIFFERENT NCS GROUPS : NULL
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 : NULL
REMARK 3 ION PROBE RADIUS : NULL
REMARK 3 SHRINKAGE RADIUS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3V4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-12.
REMARK 100 THE DEPOSITION ID IS D_1000069590.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-APR-10
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19456
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 67.110
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.09500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
REMARK 200 DATA REDUNDANCY IN SHELL : 5.30
REMARK 200 R MERGE FOR SHELL (I) : 0.53600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600
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: PDB ENTRY 2PYO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3550, 0.4 AMMONIUM NITRATE,
REMARK 280 0.1M BIS-TRIS PROPANE, VAPOR DIFFUSION, TEMPERATURE 298K, PH 7.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2
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 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
REMARK 290 7555 Y,X,-Z+1/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+2/3
REMARK 290 10555 -Y,-X,-Z+5/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+1/6
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 60.16433
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 120.32867
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 90.24650
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 150.41083
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 30.08217
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.16433
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 120.32867
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 150.41083
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 90.24650
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 30.08217
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5850 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 350 BIOMT1 2 0.500000 0.866025 0.000000 -38.75000
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 67.11697
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 30.08217
REMARK 400
REMARK 400 COMPOUND
REMARK 400
REMARK 400 THE "N-[(BENZYLOXY)CARBONYL]-L-VALYL-N~5~-[AMINO(IMINIO)METHYL]-L-
REMARK 400 ORNITHYL-N-[(3R)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-FLUORO-2-OXOHEXAN-
REMARK 400 3-YL]-L-PROLINAMIDE IS OLIGOPEPTIDE, A MEMBER OF INHIBITOR CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: "N-[(BENZYLOXY)CARBONYL]-L-VALYL-N~5~-[AMINO(IMINIO)METHYL]-
REMARK 400 L-ORNITHYL-N-[(3R)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-FLUORO-
REMARK 400 2-OXOHEXAN-3-YL]-L-PROLINAMIDE
REMARK 400 CHAIN: B
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 DESCRIPTION: NULL
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 325
REMARK 465 PRO A 326
REMARK 465 GLY A 327
REMARK 465 SER A 328
REMARK 465 ASP A 329
REMARK 465 ASN A 330
REMARK 465 LYS A 331
REMARK 465 GLU A 332
REMARK 465 GLN A 333
REMARK 465 THR A 334
REMARK 465 THR A 335
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 OG SER A 504 O HOH A 692 2.03
REMARK 500 O HOH A 636 O HOH A 745 2.08
REMARK 500 NE2 GLN A 450 O HOH A 687 2.16
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 714 O HOH A 714 12565 2.18
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 3 NE - CZ - NH2 ANGL. DEV. = -3.5 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 MET A 351 -46.21 -131.19
REMARK 500 ASP A 462 77.66 -106.40
REMARK 500 PRO A 475 -70.99 -64.90
REMARK 500 ILE A 476 56.19 33.28
REMARK 500 ASN A 485 34.04 -151.20
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG B 3 0.23 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF MALT1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3V4L RELATED DB: PDB
REMARK 900 RELATED ID: 3V55 RELATED DB: PDB
DBREF 3V4O A 329 569 UNP Q9UDY8 MALT1_HUMAN 329 569
DBREF 3V4O B 1 6 PDB 3V4O 3V4O 1 6
SEQADV 3V4O GLY A 325 UNP Q9UDY8 EXPRESSION TAG
SEQADV 3V4O PRO A 326 UNP Q9UDY8 EXPRESSION TAG
SEQADV 3V4O GLY A 327 UNP Q9UDY8 EXPRESSION TAG
SEQADV 3V4O SER A 328 UNP Q9UDY8 EXPRESSION TAG
SEQRES 1 A 245 GLY PRO GLY SER ASP ASN LYS GLU GLN THR THR ASP GLN
SEQRES 2 A 245 PRO LEU ALA LYS ASP LYS VAL ALA LEU LEU ILE GLY ASN
SEQRES 3 A 245 MET ASN TYR ARG GLU HIS PRO LYS LEU LYS ALA PRO LEU
SEQRES 4 A 245 VAL ASP VAL TYR GLU LEU THR ASN LEU LEU ARG GLN LEU
SEQRES 5 A 245 ASP PHE LYS VAL VAL SER LEU LEU ASP LEU THR GLU TYR
SEQRES 6 A 245 GLU MET ARG ASN ALA VAL ASP GLU PHE LEU LEU LEU LEU
SEQRES 7 A 245 ASP LYS GLY VAL TYR GLY LEU LEU TYR TYR ALA GLY HIS
SEQRES 8 A 245 GLY TYR GLU ASN PHE GLY ASN SER PHE MET VAL PRO VAL
SEQRES 9 A 245 ASP ALA PRO ASN PRO TYR ARG SER GLU ASN CYS LEU CYS
SEQRES 10 A 245 VAL GLN ASN ILE LEU LYS LEU MET GLN GLU LYS GLU THR
SEQRES 11 A 245 GLY LEU ASN VAL PHE LEU LEU ASP MET CYS ARG LYS ARG
SEQRES 12 A 245 ASN ASP TYR ASP ASP THR ILE PRO ILE LEU ASP ALA LEU
SEQRES 13 A 245 LYS VAL THR ALA ASN ILE VAL PHE GLY TYR ALA THR CYS
SEQRES 14 A 245 GLN GLY ALA GLU ALA PHE GLU ILE GLN HIS SER GLY LEU
SEQRES 15 A 245 ALA ASN GLY ILE PHE MET LYS PHE LEU LYS ASP ARG LEU
SEQRES 16 A 245 LEU GLU ASP LYS LYS ILE THR VAL LEU LEU ASP GLU VAL
SEQRES 17 A 245 ALA GLU ASP MET GLY LYS CYS HIS LEU THR LYS GLY LYS
SEQRES 18 A 245 GLN ALA LEU GLU ILE ARG SER SER LEU SER GLU LYS ARG
SEQRES 19 A 245 ALA LEU THR ASP PRO ILE GLN GLY THR GLU TYR
SEQRES 1 B 6 PHQ VAL ARG PRO ARG CF0
HET PHQ B 1 10
HET CF0 B 6 1
HETNAM PHQ BENZYL CHLOROCARBONATE
HETNAM CF0 FLUOROMETHANE
HETSYN CF0 FLUORO METHYL GROUP
FORMUL 2 PHQ C8 H7 CL O2
FORMUL 2 CF0 C H3 F
FORMUL 3 HOH *150(H2 O)
HELIX 1 1 ALA A 361 LEU A 376 1 16
HELIX 2 2 THR A 387 LEU A 401 1 15
HELIX 3 3 ARG A 435 CYS A 439 5 5
HELIX 4 4 VAL A 442 LYS A 452 1 11
HELIX 5 5 GLY A 509 LYS A 516 1 8
HELIX 6 6 LYS A 524 GLY A 537 1 14
HELIX 7 7 LYS A 538 LYS A 543 5 6
SHEET 1 A 6 LYS A 379 LEU A 384 0
SHEET 2 A 6 LYS A 343 GLY A 349 1 N LYS A 343 O LYS A 379
SHEET 3 A 6 TYR A 407 ALA A 413 1 O TYR A 407 N VAL A 344
SHEET 4 A 6 LEU A 456 ASP A 462 1 O ASP A 462 N TYR A 412
SHEET 5 A 6 ILE A 486 TYR A 490 1 O GLY A 489 N PHE A 459
SHEET 6 A 6 GLU A 549 SER A 552 -1 O ARG A 551 N PHE A 488
SHEET 1 B 3 GLY A 416 ASN A 419 0
SHEET 2 B 3 ASN A 422 MET A 425 -1 O PHE A 424 N TYR A 417
SHEET 3 B 3 LEU A 440 CYS A 441 -1 O LEU A 440 N MET A 425
SHEET 1 C 2 PHE A 499 GLU A 500 0
SHEET 2 C 2 ARG B 3 PRO B 4 -1 O ARG B 3 N GLU A 500
LINK SG CYS A 464 C1 CF0 B 6 1555 1555 1.88
LINK C1 PHQ B 1 N VAL B 2 1555 1555 1.34
LINK C ARG B 5 C1 CF0 B 6 1555 1555 1.51
CISPEP 1 ASN A 432 PRO A 433 0 2.82
SITE 1 AC1 19 LYS A 358 LEU A 359 ALA A 361 PRO A 362
SITE 2 AC1 19 ASP A 365 ALA A 413 GLY A 414 HIS A 415
SITE 3 AC1 19 GLY A 416 ASP A 462 CYS A 464 GLU A 497
SITE 4 AC1 19 ALA A 498 PHE A 499 GLU A 500 ILE A 501
SITE 5 AC1 19 GLN A 502 LEU A 541 HOH B 101
CRYST1 77.500 77.500 180.493 90.00 90.00 120.00 P 61 2 2 12
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 0.012903 0.007450 0.000000 0.00000
SCALE2 0.000000 0.014899 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005540 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
