HEADER LYASE 17-MAY-03 1PCW
TITLE AQUIFEX AEOLICUS KDO8PS IN COMPLEX WITH CADMIUM AND APP, A BISUBSTRATE
TITLE 2 INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: PHOSPHO-2- DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D-
COMPND 5 MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8-PHOSPHATE
COMPND 6 SYNTHETASE, KDO 8-P SYNTHASE;
COMPND 7 EC: 4.1.2.16;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS;
SOURCE 3 ORGANISM_TAXID: 63363;
SOURCE 4 GENE: KDSA OR AQ_085;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAAKDSA
KEYWDS BETA(8)/ALPHA(8) BARREL, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR X.XU,J.WANG,C.GRISON,S.PETEK,P.COUTROT,M.BIRCK,R.W.WOODARD,D.L.GATTI
REVDAT 4 16-AUG-23 1PCW 1 REMARK LINK
REVDAT 3 13-JUL-11 1PCW 1 VERSN
REVDAT 2 24-FEB-09 1PCW 1 VERSN
REVDAT 1 17-FEB-04 1PCW 0
JRNL AUTH X.XU,J.WANG,C.GRISON,S.PETEK,P.COUTROT,M.R.BIRCK,
JRNL AUTH 2 R.W.WOODARD,D.L.GATTI
JRNL TITL STRUCTURE-BASED DESIGN OF NOVEL INHIBITORS OF
JRNL TITL 2 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE.
JRNL REF DRUG DES.DISCOVERY V. 18 91 2003
JRNL REFN ISSN 1055-9612
JRNL PMID 14675946
REMARK 2
REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.47
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9
REMARK 3 NUMBER OF REFLECTIONS : 54587
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 SET) : 0.196
REMARK 3 FREE R VALUE : 0.221
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200
REMARK 3 FREE R VALUE TEST SET COUNT : 5551
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7531
REMARK 3 BIN R VALUE (WORKING SET) : 0.3280
REMARK 3 BIN FREE R VALUE : 0.3540
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 814
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4035
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 44
REMARK 3 SOLVENT ATOMS : 340
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 30.30
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.75000
REMARK 3 B22 (A**2) : 1.61000
REMARK 3 B33 (A**2) : -5.35000
REMARK 3 B12 (A**2) : 2.56000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21
REMARK 3 ESD FROM SIGMAA (A) : 0.19
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.300
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.280 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.110 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.36
REMARK 3 BSOL : 54.73
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : ION.PARAM
REMARK 3 PARAMETER FILE 3 : PEP_A5P_MOD5.PARAM
REMARK 3 PARAMETER FILE 4 : APP_MOD1.PARAM
REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : ION.TOP
REMARK 3 TOPOLOGY FILE 3 : PEP_A5P.TOPH
REMARK 3 TOPOLOGY FILE 4 : APP_MOD1.TOPH
REMARK 3 TOPOLOGY FILE 5 : WATER.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1PCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-03.
REMARK 100 THE DEPOSITION ID IS D_1000019238.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-JAN-02
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL MIRRORS
REMARK 200 OPTICS : OSMIC CONFOCAL MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54587
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 21.470
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9
REMARK 200 DATA REDUNDANCY : 11.34
REMARK 200 R MERGE (I) : 0.11700
REMARK 200 R SYM (I) : 0.11700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0
REMARK 200 DATA REDUNDANCY IN SHELL : 6.20
REMARK 200 R MERGE FOR SHELL (I) : 0.59800
REMARK 200 R SYM FOR SHELL (I) : 0.59800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.270
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: 1JCX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.28
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, PH 4.8,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K
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 53.02333
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 106.04667
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 106.04667
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 53.02333
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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED
REMARK 300 BY THE SYMMETRY OPERATION:
REMARK 300 X=Y, Y=X, Z=-Z
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,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 16470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 33570 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 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 0.00000
REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 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 MET A 1001
REMARK 465 LEU A 1193
REMARK 465 GLY A 1194
REMARK 465 ASP A 1195
REMARK 465 LYS A 1196
REMARK 465 SER A 1197
REMARK 465 GLY A 1198
REMARK 465 PRO A 1265
REMARK 465 VAL A 1266
REMARK 465 LYS A 1267
REMARK 465 MET B 2001
REMARK 465 GLU B 2002
REMARK 465 GLY B 2191
REMARK 465 GLY B 2192
REMARK 465 LEU B 2193
REMARK 465 GLY B 2194
REMARK 465 ASP B 2195
REMARK 465 LYS B 2196
REMARK 465 SER B 2197
REMARK 465 GLY B 2198
REMARK 465 PRO B 2265
REMARK 465 VAL B 2266
REMARK 465 LYS B 2267
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 GLU A1072 CD GLU A1072 OE2 0.078
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 A1042 136.29 -172.20
REMARK 500 SER B2015 146.81 173.98
REMARK 500 SER B2042 139.56 -170.70
REMARK 500 VAL B2187 66.67 -100.63
REMARK 500 MET B2200 106.08 -162.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD A1270 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A1011 SG
REMARK 620 2 HIS A1185 NE2 170.8
REMARK 620 3 GLU A1222 OE2 84.3 99.1
REMARK 620 4 GLU A1222 OE1 91.6 97.4 59.6
REMARK 620 5 ASP A1233 OD1 95.0 87.5 142.3 82.8
REMARK 620 6 H4P A1268 OA1 86.8 84.0 118.2 177.4 99.3
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD B2270 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B2011 SG
REMARK 620 2 HIS B2185 NE2 164.6
REMARK 620 3 GLU B2222 OE1 96.9 95.5
REMARK 620 4 GLU B2222 OE2 92.2 102.1 58.4
REMARK 620 5 ASP B2233 OD2 100.7 72.7 79.1 136.9
REMARK 620 6 H4P B2268 OA1 84.4 83.3 178.7 121.3 100.9
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 CD A 1270
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 2270
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H4P A 1268
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H4P B 2268
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1JCX RELATED DB: PDB
REMARK 900 AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH API AND CADMIUM
DBREF 1PCW A 1001 1267 UNP O66496 KDSA_AQUAE 1 267
DBREF 1PCW B 2001 2267 UNP O66496 KDSA_AQUAE 1 267
SEQRES 1 A 267 MET GLU LYS PHE LEU VAL ILE ALA GLY PRO CYS ALA ILE
SEQRES 2 A 267 GLU SER GLU GLU LEU LEU LEU LYS VAL GLY GLU GLU ILE
SEQRES 3 A 267 LYS ARG LEU SER GLU LYS PHE LYS GLU VAL GLU PHE VAL
SEQRES 4 A 267 PHE LYS SER SER PHE ASP LYS ALA ASN ARG SER SER ILE
SEQRES 5 A 267 HIS SER PHE ARG GLY HIS GLY LEU GLU TYR GLY VAL LYS
SEQRES 6 A 267 ALA LEU ARG LYS VAL LYS GLU GLU PHE GLY LEU LYS ILE
SEQRES 7 A 267 THR THR ASP ILE HIS GLU SER TRP GLN ALA GLU PRO VAL
SEQRES 8 A 267 ALA GLU VAL ALA ASP ILE ILE GLN ILE PRO ALA PHE LEU
SEQRES 9 A 267 CYS ARG GLN THR ASP LEU LEU LEU ALA ALA ALA LYS THR
SEQRES 10 A 267 GLY ARG ALA VAL ASN VAL LYS LYS GLY GLN PHE LEU ALA
SEQRES 11 A 267 PRO TRP ASP THR LYS ASN VAL VAL GLU LYS LEU LYS PHE
SEQRES 12 A 267 GLY GLY ALA LYS GLU ILE TYR LEU THR GLU ARG GLY THR
SEQRES 13 A 267 THR PHE GLY TYR ASN ASN LEU VAL VAL ASP PHE ARG SER
SEQRES 14 A 267 LEU PRO ILE MET LYS GLN TRP ALA LYS VAL ILE TYR ASP
SEQRES 15 A 267 ALA THR HIS SER VAL GLN LEU PRO GLY GLY LEU GLY ASP
SEQRES 16 A 267 LYS SER GLY GLY MET ARG GLU PHE ILE PHE PRO LEU ILE
SEQRES 17 A 267 ARG ALA ALA VAL ALA VAL GLY CYS ASP GLY VAL PHE MET
SEQRES 18 A 267 GLU THR HIS PRO GLU PRO GLU LYS ALA LEU SER ASP ALA
SEQRES 19 A 267 SER THR GLN LEU PRO LEU SER GLN LEU GLU GLY ILE ILE
SEQRES 20 A 267 GLU ALA ILE LEU GLU ILE ARG GLU VAL ALA SER LYS TYR
SEQRES 21 A 267 TYR GLU THR ILE PRO VAL LYS
SEQRES 1 B 267 MET GLU LYS PHE LEU VAL ILE ALA GLY PRO CYS ALA ILE
SEQRES 2 B 267 GLU SER GLU GLU LEU LEU LEU LYS VAL GLY GLU GLU ILE
SEQRES 3 B 267 LYS ARG LEU SER GLU LYS PHE LYS GLU VAL GLU PHE VAL
SEQRES 4 B 267 PHE LYS SER SER PHE ASP LYS ALA ASN ARG SER SER ILE
SEQRES 5 B 267 HIS SER PHE ARG GLY HIS GLY LEU GLU TYR GLY VAL LYS
SEQRES 6 B 267 ALA LEU ARG LYS VAL LYS GLU GLU PHE GLY LEU LYS ILE
SEQRES 7 B 267 THR THR ASP ILE HIS GLU SER TRP GLN ALA GLU PRO VAL
SEQRES 8 B 267 ALA GLU VAL ALA ASP ILE ILE GLN ILE PRO ALA PHE LEU
SEQRES 9 B 267 CYS ARG GLN THR ASP LEU LEU LEU ALA ALA ALA LYS THR
SEQRES 10 B 267 GLY ARG ALA VAL ASN VAL LYS LYS GLY GLN PHE LEU ALA
SEQRES 11 B 267 PRO TRP ASP THR LYS ASN VAL VAL GLU LYS LEU LYS PHE
SEQRES 12 B 267 GLY GLY ALA LYS GLU ILE TYR LEU THR GLU ARG GLY THR
SEQRES 13 B 267 THR PHE GLY TYR ASN ASN LEU VAL VAL ASP PHE ARG SER
SEQRES 14 B 267 LEU PRO ILE MET LYS GLN TRP ALA LYS VAL ILE TYR ASP
SEQRES 15 B 267 ALA THR HIS SER VAL GLN LEU PRO GLY GLY LEU GLY ASP
SEQRES 16 B 267 LYS SER GLY GLY MET ARG GLU PHE ILE PHE PRO LEU ILE
SEQRES 17 B 267 ARG ALA ALA VAL ALA VAL GLY CYS ASP GLY VAL PHE MET
SEQRES 18 B 267 GLU THR HIS PRO GLU PRO GLU LYS ALA LEU SER ASP ALA
SEQRES 19 B 267 SER THR GLN LEU PRO LEU SER GLN LEU GLU GLY ILE ILE
SEQRES 20 B 267 GLU ALA ILE LEU GLU ILE ARG GLU VAL ALA SER LYS TYR
SEQRES 21 B 267 TYR GLU THR ILE PRO VAL LYS
HET CD A1270 1
HET H4P A1268 21
HET CD B2270 1
HET H4P B2268 42
HETNAM CD CADMIUM ION
HETNAM H4P 1-DEOXY-6-O-PHOSPHONO-1-[(PHOSPHONOMETHYL)AMINO]-L-
HETNAM 2 H4P THREO-HEXITOL
FORMUL 3 CD 2(CD 2+)
FORMUL 4 H4P 2(C7 H19 N O11 P2)
FORMUL 7 HOH *340(H2 O)
HELIX 1 1 SER A 1015 PHE A 1033 1 19
HELIX 2 2 GLY A 1059 GLY A 1075 1 17
HELIX 3 3 GLU A 1084 TRP A 1086 5 3
HELIX 4 4 GLN A 1087 GLU A 1093 1 7
HELIX 5 5 PRO A 1101 CYS A 1105 5 5
HELIX 6 6 GLN A 1107 LYS A 1116 1 10
HELIX 7 7 ALA A 1130 ASP A 1133 5 4
HELIX 8 8 THR A 1134 GLY A 1144 1 11
HELIX 9 9 ARG A 1168 LYS A 1174 1 7
HELIX 10 10 THR A 1184 GLN A 1188 5 5
HELIX 11 11 MET A 1200 GLU A 1202 5 3
HELIX 12 12 PHE A 1203 GLY A 1215 1 13
HELIX 13 13 GLU A 1226 ALA A 1230 5 5
HELIX 14 14 GLN A 1242 LYS A 1259 1 18
HELIX 15 15 SER B 2015 PHE B 2033 1 19
HELIX 16 16 GLY B 2059 GLY B 2075 1 17
HELIX 17 17 GLU B 2084 TRP B 2086 5 3
HELIX 18 18 GLN B 2087 ALA B 2092 1 6
HELIX 19 19 PRO B 2101 CYS B 2105 5 5
HELIX 20 20 GLN B 2107 THR B 2117 1 11
HELIX 21 21 ALA B 2130 ASP B 2133 5 4
HELIX 22 22 THR B 2134 GLY B 2144 1 11
HELIX 23 23 ARG B 2168 LYS B 2174 1 7
HELIX 24 24 MET B 2200 GLU B 2202 5 3
HELIX 25 25 PHE B 2203 GLY B 2215 1 13
HELIX 26 26 GLU B 2226 ALA B 2230 5 5
HELIX 27 27 GLN B 2242 SER B 2258 1 17
HELIX 28 28 LYS B 2259 TYR B 2261 5 3
SHEET 1 A10 LEU A1238 PRO A1239 0
SHEET 2 A10 GLY A1218 HIS A1224 1 N HIS A1224 O LEU A1238
SHEET 3 A10 LYS A1178 ASP A1182 1 N TYR A1181 O PHE A1220
SHEET 4 A10 ILE A1149 GLU A1153 1 N GLU A1153 O ILE A1180
SHEET 5 A10 ALA A1120 LYS A1124 1 N VAL A1123 O THR A1152
SHEET 6 A10 ILE A1097 ILE A1100 1 N ILE A1098 O ALA A1120
SHEET 7 A10 LYS A1077 ASP A1081 1 N THR A1080 O GLN A1099
SHEET 8 A10 VAL A1036 LYS A1041 1 N PHE A1040 O LYS A1077
SHEET 9 A10 PHE A1004 GLY A1009 1 N PHE A1004 O GLU A1037
SHEET 10 A10 GLY A1218 HIS A1224 1 O VAL A1219 N ILE A1007
SHEET 1 B 2 THR A1156 THR A1157 0
SHEET 2 B 2 LEU A1163 VAL A1164 -1 O VAL A1164 N THR A1156
SHEET 1 C10 LEU B2238 PRO B2239 0
SHEET 2 C10 GLY B2218 HIS B2224 1 N HIS B2224 O LEU B2238
SHEET 3 C10 LYS B2178 ASP B2182 1 N TYR B2181 O PHE B2220
SHEET 4 C10 ILE B2149 GLU B2153 1 N GLU B2153 O ASP B2182
SHEET 5 C10 ALA B2120 LYS B2124 1 N VAL B2123 O TYR B2150
SHEET 6 C10 ILE B2097 ILE B2100 1 N ILE B2098 O ALA B2120
SHEET 7 C10 LYS B2077 ASP B2081 1 N THR B2080 O GLN B2099
SHEET 8 C10 VAL B2036 LYS B2041 1 N PHE B2040 O LYS B2077
SHEET 9 C10 PHE B2004 GLY B2009 1 N PHE B2004 O GLU B2037
SHEET 10 C10 GLY B2218 HIS B2224 1 O MET B2221 N ILE B2007
SHEET 1 D 2 THR B2156 THR B2157 0
SHEET 2 D 2 LEU B2163 VAL B2164 -1 O VAL B2164 N THR B2156
LINK SG CYS A1011 CD CD A1270 1555 1555 2.50
LINK NE2 HIS A1185 CD CD A1270 1555 1555 2.31
LINK OE2 GLU A1222 CD CD A1270 1555 1555 2.34
LINK OE1 GLU A1222 CD CD A1270 1555 1555 2.07
LINK OD1 ASP A1233 CD CD A1270 1555 1555 2.05
LINK OA1 H4P A1268 CD CD A1270 1555 1555 2.43
LINK SG CYS B2011 CD CD B2270 1555 1555 2.47
LINK NE2 HIS B2185 CD CD B2270 1555 1555 2.34
LINK OE1 GLU B2222 CD CD B2270 1555 1555 2.13
LINK OE2 GLU B2222 CD CD B2270 1555 1555 2.37
LINK OD2 ASP B2233 CD CD B2270 1555 1555 2.17
LINK OA1AH4P B2268 CD CD B2270 1555 1555 2.37
SITE 1 AC1 5 CYS A1011 HIS A1185 GLU A1222 ASP A1233
SITE 2 AC1 5 H4P A1268
SITE 1 AC2 5 CYS B2011 HIS B2185 GLU B2222 ASP B2233
SITE 2 AC2 5 H4P B2268
SITE 1 AC3 22 HOH A 13 HOH A 31 HOH A 43 HOH A 90
SITE 2 AC3 22 HOH A 201 HOH A 206 HOH A 216 HOH A 236
SITE 3 AC3 22 HOH A 359 CYS A1011 LYS A1046 ASN A1048
SITE 4 AC3 22 ARG A1049 SER A1050 PRO A1101 ALA A1102
SITE 5 AC3 22 LYS A1124 ARG A1154 HIS A1185 GLN A1188
SITE 6 AC3 22 ASP A1233 CD A1270
SITE 1 AC4 23 ARG A1106 HOH B 15 HOH B 56 HOH B 72
SITE 2 AC4 23 HOH B 93 HOH B 140 HOH B 224 HOH B 354
SITE 3 AC4 23 HOH B 373 HOH B 375 CYS B2011 LYS B2046
SITE 4 AC4 23 ASN B2048 ARG B2049 SER B2050 PRO B2101
SITE 5 AC4 23 ALA B2102 LYS B2124 ARG B2154 HIS B2185
SITE 6 AC4 23 SER B2232 ASP B2233 CD B2270
CRYST1 84.480 84.480 159.070 90.00 90.00 120.00 P 31 2 1 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 0.011837 0.006834 0.000000 0.00000
SCALE2 0.000000 0.013668 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006287 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
