PDB Short entry for 5Y3S HEADER IMMUNE SYSTEM 30-JUL-17 5Y3S TITLE CRYSTAL STRUCTURE OF HUMAN NLRP1 LEUCINE RICH REPEAT DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NACHT, LRR AND PYD DOMAINS-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 790-990; COMPND 5 SYNONYM: CASPASE RECRUITMENT DOMAIN-CONTAINING PROTEIN 7,DEATH COMPND 6 EFFECTOR FILAMENT-FORMING CED-4-LIKE APOPTOSIS PROTEIN,NUCLEOTIDE- COMPND 7 BINDING DOMAIN AND CASPASE RECRUITMENT DOMAIN; COMPND 8 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: NLRP1, CARD7, DEFCAP, KIAA0926, NAC, NALP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INFLAMMASOME, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.JIN,T.S.XIAO REVDAT 3 22-NOV-23 5Y3S 1 REMARK REVDAT 2 17-OCT-18 5Y3S 1 JRNL REMARK REVDAT 1 01-AUG-18 5Y3S 0 JRNL AUTH T.JIN,T.S.XIAO JRNL TITL CRYSTAL STRUCTURE OF HUMAN NLRP1 LRR DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2481: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 41416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2061 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 47.0679 - 6.0408 0.96 2711 124 0.1755 0.2082 REMARK 3 2 6.0408 - 4.7963 0.98 2647 141 0.2063 0.2507 REMARK 3 3 4.7963 - 4.1905 0.98 2629 131 0.1721 0.2080 REMARK 3 4 4.1905 - 3.8075 0.98 2601 146 0.1882 0.2335 REMARK 3 5 3.8075 - 3.5347 0.99 2618 129 0.2041 0.2680 REMARK 3 6 3.5347 - 3.3264 0.99 2649 132 0.2289 0.2932 REMARK 3 7 3.3264 - 3.1598 0.99 2630 129 0.2584 0.3087 REMARK 3 8 3.1598 - 3.0223 1.00 2609 134 0.2678 0.3073 REMARK 3 9 3.0223 - 2.9060 1.00 2634 139 0.2581 0.3394 REMARK 3 10 2.9060 - 2.8057 1.00 2624 143 0.2488 0.2998 REMARK 3 11 2.8057 - 2.7180 1.00 2604 131 0.2523 0.3054 REMARK 3 12 2.7180 - 2.6403 1.00 2628 149 0.2721 0.3145 REMARK 3 13 2.6403 - 2.5708 1.00 2597 136 0.2902 0.3671 REMARK 3 14 2.5708 - 2.5081 1.00 2595 151 0.2896 0.3332 REMARK 3 15 2.5081 - 2.4511 0.99 2579 146 0.2994 0.3213 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.820 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 : 0.009 6282 REMARK 3 ANGLE : 1.069 8480 REMARK 3 CHIRALITY : 0.049 1028 REMARK 3 PLANARITY : 0.005 1092 REMARK 3 DIHEDRAL : 10.110 5122 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 5Y3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 190 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41422 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.451 REMARK 200 RESOLUTION RANGE LOW (A) : 33.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05720 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.95330 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: 1DFJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM POTASSIUM PHOSPHATE, 100MM REMARK 280 HEPES, PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 70.74000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.84176 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 98.00000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 70.74000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 40.84176 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 98.00000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 70.74000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 40.84176 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 98.00000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 70.74000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 40.84176 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 98.00000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 70.74000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 40.84176 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 98.00000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 70.74000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 40.84176 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 98.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 81.68352 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 196.00000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 81.68352 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 196.00000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 81.68352 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 196.00000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 81.68352 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 196.00000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 81.68352 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 196.00000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 81.68352 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 196.00000 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 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: 9740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLY A 786 REMARK 465 SER A 787 REMARK 465 VAL A 788 REMARK 465 ASP A 789 REMARK 465 VAL A 790 REMARK 465 PRO A 791 REMARK 465 SER A 990 REMARK 465 GLY B 786 REMARK 465 SER B 787 REMARK 465 VAL B 788 REMARK 465 ASP B 789 REMARK 465 LYS B 988 REMARK 465 PRO B 989 REMARK 465 SER B 990 REMARK 465 GLY C 786 REMARK 465 LYS C 988 REMARK 465 PRO C 989 REMARK 465 SER C 990 REMARK 465 GLY D 786 REMARK 465 SER D 787 REMARK 465 ARG D 987 REMARK 465 LYS D 988 REMARK 465 PRO D 989 REMARK 465 SER D 990 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 NH1 ARG C 955 O3 PO4 C 1001 1.30 REMARK 500 O THR B 807 NH1 ARG B 836 2.03 REMARK 500 CZ ARG C 955 O3 PO4 C 1001 2.03 REMARK 500 O LYS D 805 NH2 ARG D 836 2.17 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 LEU A 981 NH2 ARG B 986 17434 2.01 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 CYS A 837 105.40 -58.64 REMARK 500 THR A 878 167.38 64.06 REMARK 500 SER A 923 -4.31 -140.45 REMARK 500 ASP A 935 -168.06 -110.92 REMARK 500 SER A 985 118.18 -163.40 REMARK 500 CYS B 837 92.31 -64.70 REMARK 500 ALA B 863 46.85 -81.89 REMARK 500 THR B 878 162.26 67.91 REMARK 500 THR B 907 -167.27 -117.43 REMARK 500 SER B 923 -28.07 -142.84 REMARK 500 ASP B 935 -158.25 -104.14 REMARK 500 VAL C 788 -70.46 -61.12 REMARK 500 THR C 793 -30.84 -35.94 REMARK 500 ASP C 794 74.41 -100.29 REMARK 500 ARG C 834 138.36 -38.10 REMARK 500 ALA C 863 63.22 -109.08 REMARK 500 THR C 878 164.28 66.13 REMARK 500 GLN C 930 155.64 -45.88 REMARK 500 ASP D 789 -159.43 -152.99 REMARK 500 THR D 878 166.15 65.59 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 NA A1002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 889 O REMARK 620 2 GLN A 891 O 88.2 REMARK 620 3 CYS A 894 O 106.5 72.7 REMARK 620 4 SER A 921 OG 67.4 152.3 125.4 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 PO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PO4 C 1001 and ARG C REMARK 800 955 DBREF 5Y3S A 790 990 UNP Q9C000 NLRP1_HUMAN 790 990 DBREF 5Y3S B 790 990 UNP Q9C000 NLRP1_HUMAN 790 990 DBREF 5Y3S C 790 990 UNP Q9C000 NLRP1_HUMAN 790 990 DBREF 5Y3S D 790 990 UNP Q9C000 NLRP1_HUMAN 790 990 SEQADV 5Y3S GLY A 786 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S SER A 787 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S VAL A 788 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S ASP A 789 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S GLY B 786 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S SER B 787 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S VAL B 788 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S ASP B 789 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S GLY C 786 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S SER C 787 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S VAL C 788 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S ASP C 789 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S GLY D 786 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S SER D 787 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S VAL D 788 UNP Q9C000 EXPRESSION TAG SEQADV 5Y3S ASP D 789 UNP Q9C000 EXPRESSION TAG SEQRES 1 A 205 GLY SER VAL ASP VAL PRO VAL THR ASP ALA TYR TRP GLN SEQRES 2 A 205 ILE LEU PHE SER VAL LEU LYS VAL THR ARG ASN LEU LYS SEQRES 3 A 205 GLU LEU ASP LEU SER GLY ASN SER LEU SER HIS SER ALA SEQRES 4 A 205 VAL LYS SER LEU CYS LYS THR LEU ARG ARG PRO ARG CYS SEQRES 5 A 205 LEU LEU GLU THR LEU ARG LEU ALA GLY CYS GLY LEU THR SEQRES 6 A 205 ALA GLU ASP CYS LYS ASP LEU ALA PHE GLY LEU ARG ALA SEQRES 7 A 205 ASN GLN THR LEU THR GLU LEU ASP LEU SER PHE ASN VAL SEQRES 8 A 205 LEU THR ASP ALA GLY ALA LYS HIS LEU CYS GLN ARG LEU SEQRES 9 A 205 ARG GLN PRO SER CYS LYS LEU GLN ARG LEU GLN LEU VAL SEQRES 10 A 205 SER CYS GLY LEU THR SER ASP CYS CYS GLN ASP LEU ALA SEQRES 11 A 205 SER VAL LEU SER ALA SER PRO SER LEU LYS GLU LEU ASP SEQRES 12 A 205 LEU GLN GLN ASN ASN LEU ASP ASP VAL GLY VAL ARG LEU SEQRES 13 A 205 LEU CYS GLU GLY LEU ARG HIS PRO ALA CYS LYS LEU ILE SEQRES 14 A 205 ARG LEU GLY LEU ASP GLN THR THR LEU SER ASP GLU MET SEQRES 15 A 205 ARG GLN GLU LEU ARG ALA LEU GLU GLN GLU LYS PRO GLN SEQRES 16 A 205 LEU LEU ILE PHE SER ARG ARG LYS PRO SER SEQRES 1 B 205 GLY SER VAL ASP VAL PRO VAL THR ASP ALA TYR TRP GLN SEQRES 2 B 205 ILE LEU PHE SER VAL LEU LYS VAL THR ARG ASN LEU LYS SEQRES 3 B 205 GLU LEU ASP LEU SER GLY ASN SER LEU SER HIS SER ALA SEQRES 4 B 205 VAL LYS SER LEU CYS LYS THR LEU ARG ARG PRO ARG CYS SEQRES 5 B 205 LEU LEU GLU THR LEU ARG LEU ALA GLY CYS GLY LEU THR SEQRES 6 B 205 ALA GLU ASP CYS LYS ASP LEU ALA PHE GLY LEU ARG ALA SEQRES 7 B 205 ASN GLN THR LEU THR GLU LEU ASP LEU SER PHE ASN VAL SEQRES 8 B 205 LEU THR ASP ALA GLY ALA LYS HIS LEU CYS GLN ARG LEU SEQRES 9 B 205 ARG GLN PRO SER CYS LYS LEU GLN ARG LEU GLN LEU VAL SEQRES 10 B 205 SER CYS GLY LEU THR SER ASP CYS CYS GLN ASP LEU ALA SEQRES 11 B 205 SER VAL LEU SER ALA SER PRO SER LEU LYS GLU LEU ASP SEQRES 12 B 205 LEU GLN GLN ASN ASN LEU ASP ASP VAL GLY VAL ARG LEU SEQRES 13 B 205 LEU CYS GLU GLY LEU ARG HIS PRO ALA CYS LYS LEU ILE SEQRES 14 B 205 ARG LEU GLY LEU ASP GLN THR THR LEU SER ASP GLU MET SEQRES 15 B 205 ARG GLN GLU LEU ARG ALA LEU GLU GLN GLU LYS PRO GLN SEQRES 16 B 205 LEU LEU ILE PHE SER ARG ARG LYS PRO SER SEQRES 1 C 205 GLY SER VAL ASP VAL PRO VAL THR ASP ALA TYR TRP GLN SEQRES 2 C 205 ILE LEU PHE SER VAL LEU LYS VAL THR ARG ASN LEU LYS SEQRES 3 C 205 GLU LEU ASP LEU SER GLY ASN SER LEU SER HIS SER ALA SEQRES 4 C 205 VAL LYS SER LEU CYS LYS THR LEU ARG ARG PRO ARG CYS SEQRES 5 C 205 LEU LEU GLU THR LEU ARG LEU ALA GLY CYS GLY LEU THR SEQRES 6 C 205 ALA GLU ASP CYS LYS ASP LEU ALA PHE GLY LEU ARG ALA SEQRES 7 C 205 ASN GLN THR LEU THR GLU LEU ASP LEU SER PHE ASN VAL SEQRES 8 C 205 LEU THR ASP ALA GLY ALA LYS HIS LEU CYS GLN ARG LEU SEQRES 9 C 205 ARG GLN PRO SER CYS LYS LEU GLN ARG LEU GLN LEU VAL SEQRES 10 C 205 SER CYS GLY LEU THR SER ASP CYS CYS GLN ASP LEU ALA SEQRES 11 C 205 SER VAL LEU SER ALA SER PRO SER LEU LYS GLU LEU ASP SEQRES 12 C 205 LEU GLN GLN ASN ASN LEU ASP ASP VAL GLY VAL ARG LEU SEQRES 13 C 205 LEU CYS GLU GLY LEU ARG HIS PRO ALA CYS LYS LEU ILE SEQRES 14 C 205 ARG LEU GLY LEU ASP GLN THR THR LEU SER ASP GLU MET SEQRES 15 C 205 ARG GLN GLU LEU ARG ALA LEU GLU GLN GLU LYS PRO GLN SEQRES 16 C 205 LEU LEU ILE PHE SER ARG ARG LYS PRO SER SEQRES 1 D 205 GLY SER VAL ASP VAL PRO VAL THR ASP ALA TYR TRP GLN SEQRES 2 D 205 ILE LEU PHE SER VAL LEU LYS VAL THR ARG ASN LEU LYS SEQRES 3 D 205 GLU LEU ASP LEU SER GLY ASN SER LEU SER HIS SER ALA SEQRES 4 D 205 VAL LYS SER LEU CYS LYS THR LEU ARG ARG PRO ARG CYS SEQRES 5 D 205 LEU LEU GLU THR LEU ARG LEU ALA GLY CYS GLY LEU THR SEQRES 6 D 205 ALA GLU ASP CYS LYS ASP LEU ALA PHE GLY LEU ARG ALA SEQRES 7 D 205 ASN GLN THR LEU THR GLU LEU ASP LEU SER PHE ASN VAL SEQRES 8 D 205 LEU THR ASP ALA GLY ALA LYS HIS LEU CYS GLN ARG LEU SEQRES 9 D 205 ARG GLN PRO SER CYS LYS LEU GLN ARG LEU GLN LEU VAL SEQRES 10 D 205 SER CYS GLY LEU THR SER ASP CYS CYS GLN ASP LEU ALA SEQRES 11 D 205 SER VAL LEU SER ALA SER PRO SER LEU LYS GLU LEU ASP SEQRES 12 D 205 LEU GLN GLN ASN ASN LEU ASP ASP VAL GLY VAL ARG LEU SEQRES 13 D 205 LEU CYS GLU GLY LEU ARG HIS PRO ALA CYS LYS LEU ILE SEQRES 14 D 205 ARG LEU GLY LEU ASP GLN THR THR LEU SER ASP GLU MET SEQRES 15 D 205 ARG GLN GLU LEU ARG ALA LEU GLU GLN GLU LYS PRO GLN SEQRES 16 D 205 LEU LEU ILE PHE SER ARG ARG LYS PRO SER HET PO4 A1001 5 HET NA A1002 1 HET PO4 C1001 5 HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION FORMUL 5 PO4 2(O4 P 3-) FORMUL 6 NA NA 1+ FORMUL 8 HOH *8(H2 O) HELIX 1 AA1 THR A 793 LYS A 805 1 13 HELIX 2 AA2 SER A 821 ARG A 834 1 14 HELIX 3 AA3 THR A 850 LEU A 861 1 12 HELIX 4 AA4 LEU A 877 ARG A 890 1 14 HELIX 5 AA5 THR A 907 ASP A 909 5 3 HELIX 6 AA6 CYS A 910 SER A 919 1 10 HELIX 7 AA7 ASP A 935 ARG A 947 1 13 HELIX 8 AA8 SER A 964 LYS A 978 1 15 HELIX 9 AA9 THR B 793 LYS B 805 1 13 HELIX 10 AB1 SER B 821 ARG B 834 1 14 HELIX 11 AB2 THR B 850 LEU B 861 1 12 HELIX 12 AB3 LEU B 877 ARG B 890 1 14 HELIX 13 AB4 THR B 907 ASP B 909 5 3 HELIX 14 AB5 CYS B 910 SER B 921 1 12 HELIX 15 AB6 ASP B 935 HIS B 948 1 14 HELIX 16 AB7 SER B 964 LYS B 978 1 15 HELIX 17 AB8 ASP C 794 THR C 807 1 14 HELIX 18 AB9 SER C 821 ARG C 834 1 14 HELIX 19 AC1 THR C 850 LEU C 861 1 12 HELIX 20 AC2 LEU C 877 ARG C 890 1 14 HELIX 21 AC3 THR C 907 ASP C 909 5 3 HELIX 22 AC4 CYS C 910 SER C 921 1 12 HELIX 23 AC5 ASP C 935 HIS C 948 1 14 HELIX 24 AC6 SER C 964 LYS C 978 1 15 HELIX 25 AC7 THR D 793 LEU D 804 1 12 HELIX 26 AC8 LYS D 805 THR D 807 5 3 HELIX 27 AC9 SER D 821 ARG D 834 1 14 HELIX 28 AD1 THR D 850 LEU D 861 1 12 HELIX 29 AD2 LEU D 877 ARG D 890 1 14 HELIX 30 AD3 THR D 907 ASP D 909 5 3 HELIX 31 AD4 CYS D 910 SER D 921 1 12 HELIX 32 AD5 ASP D 935 ARG D 947 1 13 HELIX 33 AD6 SER D 964 LYS D 978 1 15 SHEET 1 AA1 8 LEU A 982 PHE A 984 0 SHEET 2 AA1 8 ARG A 955 GLY A 957 1 N LEU A 956 O LEU A 982 SHEET 3 AA1 8 GLU A 926 ASP A 928 1 N LEU A 927 O GLY A 957 SHEET 4 AA1 8 ARG A 898 GLN A 900 1 N LEU A 899 O GLU A 926 SHEET 5 AA1 8 GLU A 869 ASP A 871 1 N LEU A 870 O GLN A 900 SHEET 6 AA1 8 THR A 841 ARG A 843 1 N LEU A 842 O ASP A 871 SHEET 7 AA1 8 GLU A 812 ASP A 814 1 N LEU A 813 O THR A 841 SHEET 8 AA1 8 THR B 807 ARG B 808 -1 O ARG B 808 N GLU A 812 SHEET 1 AA2 7 GLU B 812 ASP B 814 0 SHEET 2 AA2 7 THR B 841 ARG B 843 1 O ARG B 843 N LEU B 813 SHEET 3 AA2 7 GLU B 869 ASP B 871 1 O GLU B 869 N LEU B 842 SHEET 4 AA2 7 ARG B 898 GLN B 900 1 O ARG B 898 N LEU B 870 SHEET 5 AA2 7 GLU B 926 ASP B 928 1 O GLU B 926 N LEU B 899 SHEET 6 AA2 7 ARG B 955 GLY B 957 1 O GLY B 957 N LEU B 927 SHEET 7 AA2 7 LEU B 982 PHE B 984 1 O PHE B 984 N LEU B 956 SHEET 1 AA3 7 GLU C 812 ASP C 814 0 SHEET 2 AA3 7 THR C 841 ARG C 843 1 O ARG C 843 N LEU C 813 SHEET 3 AA3 7 GLU C 869 ASP C 871 1 O GLU C 869 N LEU C 842 SHEET 4 AA3 7 ARG C 898 GLN C 900 1 O ARG C 898 N LEU C 870 SHEET 5 AA3 7 GLU C 926 ASP C 928 1 O ASP C 928 N LEU C 899 SHEET 6 AA3 7 ARG C 955 GLY C 957 1 O ARG C 955 N LEU C 927 SHEET 7 AA3 7 LEU C 982 PHE C 984 1 O LEU C 982 N LEU C 956 SHEET 1 AA4 7 GLU D 812 ASP D 814 0 SHEET 2 AA4 7 THR D 841 ARG D 843 1 O ARG D 843 N LEU D 813 SHEET 3 AA4 7 GLU D 869 ASP D 871 1 O GLU D 869 N LEU D 842 SHEET 4 AA4 7 ARG D 898 GLN D 900 1 O ARG D 898 N LEU D 870 SHEET 5 AA4 7 GLU D 926 ASP D 928 1 O GLU D 926 N LEU D 899 SHEET 6 AA4 7 ARG D 955 GLY D 957 1 O GLY D 957 N LEU D 927 SHEET 7 AA4 7 LEU D 982 PHE D 984 1 O PHE D 984 N LEU D 956 LINK O LEU A 889 NA NA A1002 1555 1555 2.51 LINK O GLN A 891 NA NA A1002 1555 1555 2.57 LINK O CYS A 894 NA NA A1002 1555 1555 3.17 LINK OG SER A 921 NA NA A1002 1555 1555 3.01 SITE 1 AC1 3 LYS A 883 ASP A 913 ARG D 833 SITE 1 AC2 6 LEU A 889 GLN A 891 CYS A 894 ALA A 920 SITE 2 AC2 6 SER A 921 PRO A 922 SITE 1 AC3 11 THR A 961 ARG A 987 LYS A 988 PRO A 989 SITE 2 AC3 11 LYS C 925 GLU C 926 LEU C 927 LEU C 953 SITE 3 AC3 11 ILE C 954 LEU C 956 LEU C 982 CRYST1 141.480 141.480 294.000 90.00 90.00 120.00 H 3 2 72 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 0.007068 0.004081 0.000000 0.00000 SCALE2 0.000000 0.008162 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003401 0.00000