HEADER HYDROLASE/HYDROLASE INHIBITOR 08-JUN-20 6XCI TITLE STRUCTURE OF NDM-1 IN COMPLEX WITH MACROCYCLE INHIBITOR NDM1I-3D COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLANDM-4_1_JQ348841; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: METALLO BETA-LACTAMASE,METALLO-BETA-LACTAMASE NDM-1,METALLO- COMPND 5 BETA-LACTAMASE,NDM-1,NDM1 METALLO-BETA-LACTAMASE,NEW DELHI METALLO COMPND 6 CARBAPENEMASE-1,NEW DELHI METALLO-BETA-LACTAMASE NDM-1,NEW DELHI COMPND 7 METALLO-BETA-LACTAMSE 1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MACROCYCLE NDM1I-3D; COMPND 11 CHAIN: H; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: MACROCYCLE / CYCLIC PEPTIDE SEQUENCE: D-CYSTEINE COMPND 14 PROLINE 2-AMINOMETHYL-L-PHENYLALANINE (LWI CIF) HYDROXYPROLINE COMPND 15 GLUTAMATE D-PROLINE D-LYSINE NORLEUCINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: NDM-1, BLA NDM-1, BLANDM-1, BLANDM1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS CYCLIC PEPTIDE, MACROCYCLE INHIBITOR, ANTIBIOTIC, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.J.WORRALL,T.SUN,V.K.MULLIGAN,N.C.J.STRYNADKA REVDAT 3 15-NOV-23 6XCI 1 LINK REVDAT 2 18-OCT-23 6XCI 1 REMARK REVDAT 1 31-MAR-21 6XCI 0 JRNL AUTH V.K.MULLIGAN,S.WORKMAN,T.SUN,S.RETTIE,X.LI,L.J.WORRALL, JRNL AUTH 2 T.W.CRAVEN,D.T.KING,P.HOSSEINZADEH,A.M.WATKINS,P.D.RENFREW, JRNL AUTH 3 S.GUFFY,J.W.LABONTE,R.MORETTI,R.BONNEAU,N.C.J.STRYNADKA, JRNL AUTH 4 D.BAKER JRNL TITL COMPUTATIONALLY DESIGNED PEPTIDE MACROCYCLE INHIBITORS OF JRNL TITL 2 NEW DELHI METALLO-BETA-LACTAMASE 1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33723038 JRNL DOI 10.1073/PNAS.2012800118 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 46797 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) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2688 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1315 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 35.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 356 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.08000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.334 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3545 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3230 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4839 ; 1.694 ; 1.633 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7497 ; 1.571 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 6.714 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;30.510 ;23.395 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 522 ;13.603 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.462 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 476 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4078 ; 0.010 ; 0.020 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 B 42 269 A 42 269 7073 0.090 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6XCI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-18 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49546 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 4EXS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 2000 MONOMETHYL ETHER, 0.1M REMARK 280 MES, PH 6.5 AND 200MM NACL), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 35.58400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.82700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.89450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.82700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.58400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.89450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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: 2 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: NULL REMARK 400 CHAIN: H 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 B 23 REMARK 465 SER B 24 REMARK 465 HIS B 25 REMARK 465 MET B 26 REMARK 465 MET B 27 REMARK 465 PRO B 28 REMARK 465 GLY B 29 REMARK 465 GLU B 30 REMARK 465 ILE B 31 REMARK 465 ARG B 32 REMARK 465 PRO B 33 REMARK 465 THR B 34 REMARK 465 ILE B 35 REMARK 465 GLY B 36 REMARK 465 GLN B 37 REMARK 465 GLN B 38 REMARK 465 MET B 39 REMARK 465 GLU B 40 REMARK 465 THR B 41 REMARK 465 MET B 67 REMARK 465 PRO B 68 REMARK 465 GLY B 69 REMARK 465 PHE B 70 REMARK 465 ARG B 270 REMARK 465 GLY A 23 REMARK 465 SER A 24 REMARK 465 HIS A 25 REMARK 465 MET A 26 REMARK 465 MET A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 ILE A 31 REMARK 465 ARG A 32 REMARK 465 PRO A 33 REMARK 465 THR A 34 REMARK 465 ILE A 35 REMARK 465 GLY A 36 REMARK 465 GLN A 37 REMARK 465 GLN A 38 REMARK 465 MET A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 ARG A 270 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 488 O HOH B 533 2.02 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 B 90 143.23 76.35 REMARK 500 ASP A 90 142.66 77.87 REMARK 500 HIS A 120 167.30 179.14 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 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 122 ND1 REMARK 620 2 HIS B 189 NE2 109.4 REMARK 620 3 HOH B 404 O 111.2 110.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 303 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 94.6 REMARK 620 3 HIS B 250 NE2 82.2 105.3 REMARK 620 4 HOH B 404 O 83.2 98.5 152.9 REMARK 620 5 HOH B 556 O 161.8 103.4 90.2 96.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 304 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 152 OE1 REMARK 620 2 GLU B 152 OE2 55.2 REMARK 620 3 ASP B 223 OD2 91.8 95.8 REMARK 620 4 HOH B 554 O 87.2 138.4 103.4 REMARK 620 5 GLU A 227 OE1 144.6 89.4 91.9 125.8 REMARK 620 6 GLU A 227 OE2 115.2 84.7 146.2 98.1 54.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 305 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 227 OE1 REMARK 620 2 GLU B 227 OE2 53.9 REMARK 620 3 GLU A 152 OE1 118.0 143.2 REMARK 620 4 GLU A 152 OE2 86.9 88.8 54.5 REMARK 620 5 ASP A 223 OD2 145.4 91.5 88.7 92.6 REMARK 620 6 HOH A 547 O 97.2 127.0 88.0 138.0 105.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 103.0 REMARK 620 3 HIS A 189 NE2 102.7 109.7 REMARK 620 4 HOH H 101 O 115.9 109.3 115.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 92.4 REMARK 620 3 HIS A 250 NE2 82.7 104.2 REMARK 620 4 HOH A 545 O 164.2 103.0 90.2 REMARK 620 5 GLU H 5 OE2 81.3 165.8 87.6 84.4 REMARK 620 6 HOH H 101 O 78.8 90.1 157.0 104.1 76.2 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 ACT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for ? chain H REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XBE RELATED DB: PDB REMARK 900 6XBE CONTAINS SAME PROTEIN COMPLEXED WITH NDM1I-1F REMARK 900 RELATED ID: 6XBF RELATED DB: PDB REMARK 900 6XBF CONTAINS SAME PROTEIN COMPLEXED WITH NDM1I-1G DBREF 6XCI B 27 270 UNP E9NWK5 E9NWK5_KLEPN 27 270 DBREF 6XCI A 27 270 UNP E9NWK5 E9NWK5_KLEPN 27 270 DBREF 6XCI H 1 8 PDB 6XCI 6XCI 1 8 SEQADV 6XCI GLY B 23 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI SER B 24 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI HIS B 25 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI MET B 26 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI GLY A 23 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI SER A 24 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI HIS A 25 UNP E9NWK5 EXPRESSION TAG SEQADV 6XCI MET A 26 UNP E9NWK5 EXPRESSION TAG SEQRES 1 B 248 GLY SER HIS MET MET PRO GLY GLU ILE ARG PRO THR ILE SEQRES 2 B 248 GLY GLN GLN MET GLU THR GLY ASP GLN ARG PHE GLY ASP SEQRES 3 B 248 LEU VAL PHE ARG GLN LEU ALA PRO ASN VAL TRP GLN HIS SEQRES 4 B 248 THR SER TYR LEU ASP MET PRO GLY PHE GLY ALA VAL ALA SEQRES 5 B 248 SER ASN GLY LEU ILE VAL ARG ASP GLY GLY ARG VAL LEU SEQRES 6 B 248 VAL VAL ASP THR ALA TRP THR ASP ASP GLN THR ALA GLN SEQRES 7 B 248 ILE LEU ASN TRP ILE LYS GLN GLU ILE ASN LEU PRO VAL SEQRES 8 B 248 ALA LEU ALA VAL VAL THR HIS ALA HIS GLN ASP LYS MET SEQRES 9 B 248 GLY GLY MET ASP ALA LEU HIS ALA ALA GLY ILE ALA THR SEQRES 10 B 248 TYR ALA ASN ALA LEU SER ASN GLN LEU ALA PRO GLN GLU SEQRES 11 B 248 GLY MET VAL ALA ALA GLN HIS SER LEU THR PHE ALA ALA SEQRES 12 B 248 ASN GLY TRP VAL GLU PRO ALA THR ALA PRO ASN PHE GLY SEQRES 13 B 248 PRO LEU LYS VAL PHE TYR PRO GLY PRO GLY HIS THR SER SEQRES 14 B 248 ASP ASN ILE THR VAL GLY ILE ASP GLY THR ASP ILE ALA SEQRES 15 B 248 PHE GLY GLY CYS LEU ILE LYS ASP SER LYS ALA LYS SER SEQRES 16 B 248 LEU GLY ASN LEU GLY ASP ALA ASP THR GLU HIS TYR ALA SEQRES 17 B 248 ALA SER ALA ARG ALA PHE GLY ALA ALA PHE PRO LYS ALA SEQRES 18 B 248 SER MET ILE VAL MET SER HIS SER ALA PRO ASP SER ARG SEQRES 19 B 248 ALA ALA ILE THR HIS THR ALA ARG MET ALA ASP LYS LEU SEQRES 20 B 248 ARG SEQRES 1 A 248 GLY SER HIS MET MET PRO GLY GLU ILE ARG PRO THR ILE SEQRES 2 A 248 GLY GLN GLN MET GLU THR GLY ASP GLN ARG PHE GLY ASP SEQRES 3 A 248 LEU VAL PHE ARG GLN LEU ALA PRO ASN VAL TRP GLN HIS SEQRES 4 A 248 THR SER TYR LEU ASP MET PRO GLY PHE GLY ALA VAL ALA SEQRES 5 A 248 SER ASN GLY LEU ILE VAL ARG ASP GLY GLY ARG VAL LEU SEQRES 6 A 248 VAL VAL ASP THR ALA TRP THR ASP ASP GLN THR ALA GLN SEQRES 7 A 248 ILE LEU ASN TRP ILE LYS GLN GLU ILE ASN LEU PRO VAL SEQRES 8 A 248 ALA LEU ALA VAL VAL THR HIS ALA HIS GLN ASP LYS MET SEQRES 9 A 248 GLY GLY MET ASP ALA LEU HIS ALA ALA GLY ILE ALA THR SEQRES 10 A 248 TYR ALA ASN ALA LEU SER ASN GLN LEU ALA PRO GLN GLU SEQRES 11 A 248 GLY MET VAL ALA ALA GLN HIS SER LEU THR PHE ALA ALA SEQRES 12 A 248 ASN GLY TRP VAL GLU PRO ALA THR ALA PRO ASN PHE GLY SEQRES 13 A 248 PRO LEU LYS VAL PHE TYR PRO GLY PRO GLY HIS THR SER SEQRES 14 A 248 ASP ASN ILE THR VAL GLY ILE ASP GLY THR ASP ILE ALA SEQRES 15 A 248 PHE GLY GLY CYS LEU ILE LYS ASP SER LYS ALA LYS SER SEQRES 16 A 248 LEU GLY ASN LEU GLY ASP ALA ASP THR GLU HIS TYR ALA SEQRES 17 A 248 ALA SER ALA ARG ALA PHE GLY ALA ALA PHE PRO LYS ALA SEQRES 18 A 248 SER MET ILE VAL MET SER HIS SER ALA PRO ASP SER ARG SEQRES 19 A 248 ALA ALA ILE THR HIS THR ALA ARG MET ALA ASP LYS LEU SEQRES 20 A 248 ARG SEQRES 1 H 8 DCY PRO LWI HYP GLU DPR DLY NLE HET DCY H 1 6 HET LWI H 3 13 HET HYP H 4 8 HET DPR H 6 7 HET DLY H 7 9 HET NLE H 8 8 HET ACT B 301 4 HET ZN B 302 1 HET CD B 303 1 HET CD B 304 1 HET CD B 305 1 HET ZN A 301 1 HET CD A 302 1 HETNAM DCY D-CYSTEINE HETNAM LWI 2-(AMINOMETHYL)-L-PHENYLALANINE HETNAM HYP 4-HYDROXYPROLINE HETNAM DPR D-PROLINE HETNAM DLY D-LYSINE HETNAM NLE NORLEUCINE HETNAM ACT ACETATE ION HETNAM ZN ZINC ION HETNAM CD CADMIUM ION HETSYN HYP HYDROXYPROLINE FORMUL 3 DCY C3 H7 N O2 S FORMUL 3 LWI C10 H14 N2 O2 FORMUL 3 HYP C5 H9 N O3 FORMUL 3 DPR C5 H9 N O2 FORMUL 3 DLY C6 H14 N2 O2 FORMUL 3 NLE C6 H13 N O2 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 ZN 2(ZN 2+) FORMUL 6 CD 4(CD 2+) FORMUL 11 HOH *356(H2 O) HELIX 1 AA1 THR B 94 ILE B 109 1 16 HELIX 2 AA2 HIS B 122 GLY B 127 1 6 HELIX 3 AA3 GLY B 128 ALA B 135 1 8 HELIX 4 AA4 ALA B 143 ALA B 149 1 7 HELIX 5 AA5 PRO B 150 GLY B 153 5 4 HELIX 6 AA6 GLU B 170 ALA B 174 5 5 HELIX 7 AA7 HIS B 228 PHE B 240 1 13 HELIX 8 AA8 ARG B 256 LYS B 268 1 13 HELIX 9 AA9 THR A 94 ILE A 109 1 16 HELIX 10 AB1 HIS A 122 GLY A 127 1 6 HELIX 11 AB2 GLY A 128 ALA A 135 1 8 HELIX 12 AB3 ALA A 143 GLY A 153 1 11 HELIX 13 AB4 GLU A 170 ALA A 174 5 5 HELIX 14 AB5 HIS A 228 PHE A 240 1 13 HELIX 15 AB6 ARG A 256 LYS A 268 1 13 HELIX 16 AB7 HYP H 4 NLE H 8 5 5 SHEET 1 AA1 8 ASP B 43 PHE B 46 0 SHEET 2 AA1 8 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 3 AA1 8 VAL B 58 LEU B 65 -1 O GLN B 60 N ARG B 52 SHEET 4 AA1 8 VAL B 73 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 5 AA1 8 ARG B 85 VAL B 89 -1 O VAL B 89 N LEU B 78 SHEET 6 AA1 8 VAL B 113 VAL B 117 1 O VAL B 117 N VAL B 88 SHEET 7 AA1 8 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 8 AA1 8 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 AA2 4 LEU B 180 PHE B 183 0 SHEET 2 AA2 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 AA2 4 ILE B 203 PHE B 205 -1 O PHE B 205 N VAL B 196 SHEET 4 AA2 4 MET B 245 VAL B 247 1 O VAL B 247 N ALA B 204 SHEET 1 AA3 8 GLN A 44 PHE A 46 0 SHEET 2 AA3 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 AA3 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 AA3 8 GLY A 71 ASP A 82 -1 O VAL A 73 N LEU A 65 SHEET 5 AA3 8 ARG A 85 VAL A 89 -1 O VAL A 89 N LEU A 78 SHEET 6 AA3 8 VAL A 113 VAL A 117 1 O VAL A 117 N VAL A 88 SHEET 7 AA3 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA3 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA4 4 LEU A 180 PHE A 183 0 SHEET 2 AA4 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 AA4 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 AA4 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 LINK C DCY H 1 N PRO H 2 1555 1555 1.36 LINK N DCY H 1 C NLE H 8 1555 1555 1.35 LINK C PRO H 2 N LWI H 3 1555 1555 1.35 LINK C LWI H 3 N HYP H 4 1555 1555 1.35 LINK C HYP H 4 N GLU H 5 1555 1555 1.34 LINK C GLU H 5 N DPR H 6 1555 1555 1.36 LINK C DPR H 6 N DLY H 7 1555 1555 1.34 LINK C DLY H 7 N NLE H 8 1555 1555 1.34 LINK ND1 HIS B 122 ZN ZN B 302 1555 1555 2.03 LINK OD2 ASP B 124 CD CD B 303 1555 1555 2.23 LINK OE1 GLU B 152 CD CD B 304 1555 1555 2.51 LINK OE2 GLU B 152 CD CD B 304 1555 1555 2.34 LINK NE2 HIS B 189 ZN ZN B 302 1555 1555 2.01 LINK SG CYS B 208 CD CD B 303 1555 1555 2.50 LINK OD2 ASP B 223 CD CD B 304 1555 1555 2.20 LINK OE1 GLU B 227 CD CD B 305 1555 1555 2.33 LINK OE2 GLU B 227 CD CD B 305 1555 1555 2.36 LINK NE2 HIS B 250 CD CD B 303 1555 1555 2.22 LINK ZN ZN B 302 O HOH B 404 1555 1555 1.94 LINK CD CD B 303 O HOH B 404 1555 1555 2.31 LINK CD CD B 303 O HOH B 556 1555 1555 2.65 LINK CD CD B 304 O HOH B 554 1555 1555 2.32 LINK CD CD B 304 OE1 GLU A 227 1555 1555 2.31 LINK CD CD B 304 OE2 GLU A 227 1555 1555 2.35 LINK CD CD B 305 OE1 GLU A 152 1555 1555 2.51 LINK CD CD B 305 OE2 GLU A 152 1555 1555 2.39 LINK CD CD B 305 OD2 ASP A 223 1555 1555 2.24 LINK CD CD B 305 O HOH A 547 1555 1555 2.39 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.06 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.04 LINK OD2 ASP A 124 CD CD A 302 1555 1555 2.31 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.00 LINK SG CYS A 208 CD CD A 302 1555 1555 2.53 LINK NE2 HIS A 250 CD CD A 302 1555 1555 2.22 LINK ZN ZN A 301 O HOH H 101 1555 1555 1.97 LINK CD CD A 302 O HOH A 545 1555 1555 2.66 LINK CD CD A 302 OE2 GLU H 5 1555 1555 2.46 LINK CD CD A 302 O HOH H 101 1555 1555 2.42 CISPEP 1 GLY B 219 ASN B 220 0 5.57 SITE 1 AC1 7 HIS B 122 ASP B 124 ASN B 220 ZN B 302 SITE 2 AC1 7 CD B 303 HOH B 404 HOH B 530 SITE 1 AC2 5 HIS B 120 HIS B 122 HIS B 189 ACT B 301 SITE 2 AC2 5 HOH B 404 SITE 1 AC3 6 ASP B 124 CYS B 208 HIS B 250 ACT B 301 SITE 2 AC3 6 HOH B 404 HOH B 556 SITE 1 AC4 4 GLU A 227 GLU B 152 ASP B 223 HOH B 554 SITE 1 AC5 4 GLU A 152 ASP A 223 HOH A 547 GLU B 227 SITE 1 AC6 4 HIS A 120 HIS A 122 HIS A 189 HOH H 101 SITE 1 AC7 6 ASP A 124 CYS A 208 HIS A 250 HOH A 545 SITE 2 AC7 6 GLU H 5 HOH H 101 SITE 1 AC8 12 MET A 67 PRO A 68 PHE A 70 VAL A 73 SITE 2 AC8 12 ASP A 124 GLY A 219 ASN A 220 HIS A 250 SITE 3 AC8 12 CD A 302 GLY B 71 LYS B 216 HOH H 101 CRYST1 71.168 73.789 77.654 90.00 90.00 90.00 P 21 21 21 8 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 0.014051 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012878 0.00000