HEADER TRANSFERASE/TRANSFERASE INHIBITOR 24-MAY-16 5K69 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS L,D-TRANSPEPTIDASE 2 TITLE 2 WITH CARBAPENEM DRUG T224 COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LDT 2,LDT(MT2); COMPND 5 EC: 2.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: LDTB, LPPS, RV2518C, RVBD_2518C, P425_02624; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET38A KEYWDS PEPTIDASE, IGD_LIKE DOMAIN, YKUD DOMAIN, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.LAMICHHANE,S.L.GINELL,P.KUMAR REVDAT 6 27-SEP-23 5K69 1 REMARK REVDAT 5 11-DEC-19 5K69 1 REMARK REVDAT 4 20-SEP-17 5K69 1 REMARK REVDAT 3 28-DEC-16 5K69 1 JRNL REVDAT 2 23-NOV-16 5K69 1 JRNL REVDAT 1 09-NOV-16 5K69 0 JRNL AUTH P.KUMAR,A.KAUSHIK,E.P.LLOYD,S.G.LI,R.MATTOO,N.C.AMMERMAN, JRNL AUTH 2 D.T.BELL,A.L.PERRYMAN,T.A.ZANDI,S.EKINS,S.L.GINELL, JRNL AUTH 3 C.A.TOWNSEND,J.S.FREUNDLICH,G.LAMICHHANE JRNL TITL NON-CLASSICAL TRANSPEPTIDASES YIELD INSIGHT INTO NEW JRNL TITL 2 ANTIBACTERIALS. JRNL REF NAT. CHEM. BIOL. V. 13 54 2017 JRNL REFN ESSN 1552-4469 JRNL PMID 27820797 JRNL DOI 10.1038/NCHEMBIO.2237 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 61.7 REMARK 3 NUMBER OF REFLECTIONS : 70044 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.580 REMARK 3 FREE R VALUE TEST SET COUNT : 2506 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 28.9831 - 5.2344 0.93 5651 208 0.1686 0.1679 REMARK 3 2 5.2344 - 4.1586 0.88 5321 198 0.1529 0.1911 REMARK 3 3 4.1586 - 3.6341 0.85 5184 198 0.1733 0.2356 REMARK 3 4 3.6341 - 3.3023 0.81 4920 189 0.1887 0.2382 REMARK 3 5 3.3023 - 3.0659 0.77 4689 171 0.2040 0.2166 REMARK 3 6 3.0659 - 2.8853 0.72 4391 150 0.2205 0.2603 REMARK 3 7 2.8853 - 2.7409 0.66 4004 150 0.2198 0.2494 REMARK 3 8 2.7409 - 2.6217 0.60 3625 131 0.2247 0.2736 REMARK 3 9 2.6217 - 2.5208 0.53 3248 121 0.2357 0.2874 REMARK 3 10 2.5208 - 2.4339 0.51 3120 122 0.2278 0.2570 REMARK 3 11 2.4339 - 2.3578 0.50 3047 113 0.2334 0.2346 REMARK 3 12 2.3578 - 2.2905 0.50 3013 112 0.2268 0.2665 REMARK 3 13 2.2905 - 2.2302 0.49 2991 111 0.2235 0.3007 REMARK 3 14 2.2302 - 2.1758 0.49 3004 112 0.2263 0.2915 REMARK 3 15 2.1758 - 2.1263 0.49 2970 102 0.2203 0.2459 REMARK 3 16 2.1263 - 2.0811 0.49 2921 123 0.2232 0.2413 REMARK 3 17 2.0811 - 2.0395 0.47 2904 101 0.2256 0.2748 REMARK 3 18 2.0395 - 2.0010 0.42 2535 94 0.2331 0.2731 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.250 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 : 0.004 5478 REMARK 3 ANGLE : 0.864 7500 REMARK 3 CHIRALITY : 0.033 839 REMARK 3 PLANARITY : 0.004 981 REMARK 3 DIHEDRAL : 11.407 1895 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 5K69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221798. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70044 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 14.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5DU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG5000MME, AMMONIUM SULFATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 47.07500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 48.47466 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -47.07500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 226.53622 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 1 REMARK 465 PRO A 2 REMARK 465 LYS A 3 REMARK 465 VAL A 4 REMARK 465 GLY A 5 REMARK 465 ILE A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 GLN A 9 REMARK 465 ALA A 10 REMARK 465 GLY A 11 REMARK 465 ARG A 12 REMARK 465 THR A 13 REMARK 465 ARG A 14 REMARK 465 VAL A 15 REMARK 465 ARG A 16 REMARK 465 ARG A 17 REMARK 465 ALA A 18 REMARK 465 TRP A 19 REMARK 465 LEU A 20 REMARK 465 THR A 21 REMARK 465 ALA A 22 REMARK 465 LEU A 23 REMARK 465 MET A 24 REMARK 465 MET A 25 REMARK 465 THR A 26 REMARK 465 ALA A 27 REMARK 465 VAL A 28 REMARK 465 MET A 29 REMARK 465 ILE A 30 REMARK 465 GLY A 31 REMARK 465 ALA A 32 REMARK 465 VAL A 33 REMARK 465 ALA A 34 REMARK 465 CYS A 35 REMARK 465 GLY A 36 REMARK 465 SER A 37 REMARK 465 GLY A 38 REMARK 465 ARG A 39 REMARK 465 GLY A 40 REMARK 465 PRO A 41 REMARK 465 ALA A 42 REMARK 465 PRO A 43 REMARK 465 ILE A 44 REMARK 465 LYS A 45 REMARK 465 VAL A 46 REMARK 465 ILE A 47 REMARK 465 ALA A 48 REMARK 465 ASP A 49 REMARK 465 LYS A 50 REMARK 465 GLY A 51 REMARK 465 THR A 52 REMARK 465 PRO A 53 REMARK 465 PHE A 54 REMARK 465 ALA A 55 REMARK 465 ASP A 56 REMARK 465 LEU A 57 REMARK 465 ALA A 408 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 LYS B 3 REMARK 465 VAL B 4 REMARK 465 GLY B 5 REMARK 465 ILE B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 GLN B 9 REMARK 465 ALA B 10 REMARK 465 GLY B 11 REMARK 465 ARG B 12 REMARK 465 THR B 13 REMARK 465 ARG B 14 REMARK 465 VAL B 15 REMARK 465 ARG B 16 REMARK 465 ARG B 17 REMARK 465 ALA B 18 REMARK 465 TRP B 19 REMARK 465 LEU B 20 REMARK 465 THR B 21 REMARK 465 ALA B 22 REMARK 465 LEU B 23 REMARK 465 MET B 24 REMARK 465 MET B 25 REMARK 465 THR B 26 REMARK 465 ALA B 27 REMARK 465 VAL B 28 REMARK 465 MET B 29 REMARK 465 ILE B 30 REMARK 465 GLY B 31 REMARK 465 ALA B 32 REMARK 465 VAL B 33 REMARK 465 ALA B 34 REMARK 465 CYS B 35 REMARK 465 GLY B 36 REMARK 465 SER B 37 REMARK 465 GLY B 38 REMARK 465 ARG B 39 REMARK 465 GLY B 40 REMARK 465 PRO B 41 REMARK 465 ALA B 42 REMARK 465 PRO B 43 REMARK 465 ILE B 44 REMARK 465 LYS B 45 REMARK 465 VAL B 46 REMARK 465 ILE B 47 REMARK 465 ALA B 48 REMARK 465 ASP B 49 REMARK 465 LYS B 50 REMARK 465 GLY B 51 REMARK 465 THR B 52 REMARK 465 PRO B 53 REMARK 465 PHE B 54 REMARK 465 ALA B 55 REMARK 465 ASP B 56 REMARK 465 LEU B 57 REMARK 465 LYS B 407 REMARK 465 ALA B 408 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 OG1 THR A 228 O HOH A 601 2.11 REMARK 500 OD2 ASP B 96 O HOH B 601 2.15 REMARK 500 NH1 ARG B 99 O HOH B 602 2.16 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 ASN A 227 67.48 -101.17 REMARK 500 HIS A 347 -58.28 -137.01 REMARK 500 ASN A 405 45.43 -146.85 REMARK 500 ASN B 97 -36.16 -34.06 REMARK 500 HIS B 347 -50.89 -134.64 REMARK 500 ASN B 405 38.76 -146.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 6QR A 503 REMARK 615 6QR B 502 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6QR A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 6QR B 502 and CYS B REMARK 800 354 DBREF 5K69 A 1 408 UNP I6Y9J2 LDT2_MYCTU 1 408 DBREF 5K69 B 1 408 UNP I6Y9J2 LDT2_MYCTU 1 408 SEQRES 1 A 408 MET PRO LYS VAL GLY ILE ALA ALA GLN ALA GLY ARG THR SEQRES 2 A 408 ARG VAL ARG ARG ALA TRP LEU THR ALA LEU MET MET THR SEQRES 3 A 408 ALA VAL MET ILE GLY ALA VAL ALA CYS GLY SER GLY ARG SEQRES 4 A 408 GLY PRO ALA PRO ILE LYS VAL ILE ALA ASP LYS GLY THR SEQRES 5 A 408 PRO PHE ALA ASP LEU LEU VAL PRO LYS LEU THR ALA SER SEQRES 6 A 408 VAL THR ASP GLY ALA VAL GLY VAL THR VAL ASP ALA PRO SEQRES 7 A 408 VAL SER VAL THR ALA ALA ASP GLY VAL LEU ALA ALA VAL SEQRES 8 A 408 THR MET VAL ASN ASP ASN GLY ARG PRO VAL ALA GLY ARG SEQRES 9 A 408 LEU SER PRO ASP GLY LEU ARG TRP SER THR THR GLU GLN SEQRES 10 A 408 LEU GLY TYR ASN ARG ARG TYR THR LEU ASN ALA THR ALA SEQRES 11 A 408 LEU GLY LEU GLY GLY ALA ALA THR ARG GLN LEU THR PHE SEQRES 12 A 408 GLN THR SER SER PRO ALA HIS LEU THR MET PRO TYR VAL SEQRES 13 A 408 MET PRO GLY ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO SEQRES 14 A 408 VAL ALA ILE ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY SEQRES 15 A 408 ALA ALA GLU LYS ALA ILE LYS ILE THR THR ASN PRO PRO SEQRES 16 A 408 VAL GLU GLY ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL SEQRES 17 A 408 ARG TRP ARG PRO GLU HIS PHE TRP LYS PRO GLY THR ALA SEQRES 18 A 408 VAL ASP VAL ALA VAL ASN THR TYR GLY VAL ASP LEU GLY SEQRES 19 A 408 GLU GLY MET PHE GLY GLU ASP ASN VAL GLN THR HIS PHE SEQRES 20 A 408 THR ILE GLY ASP GLU VAL ILE ALA THR ALA ASP ASP ASN SEQRES 21 A 408 THR LYS ILE LEU THR VAL ARG VAL ASN GLY GLU VAL VAL SEQRES 22 A 408 LYS SER MET PRO THR SER MET GLY LYS ASP SER THR PRO SEQRES 23 A 408 THR ALA ASN GLY ILE TYR ILE VAL GLY SER ARG TYR LYS SEQRES 24 A 408 HIS ILE ILE MET ASP SER SER THR TYR GLY VAL PRO VAL SEQRES 25 A 408 ASN SER PRO ASN GLY TYR ARG THR ASP VAL ASP TRP ALA SEQRES 26 A 408 THR GLN ILE SER TYR SER GLY VAL PHE VAL HIS SER ALA SEQRES 27 A 408 PRO TRP SER VAL GLY ALA GLN GLY HIS THR ASN THR SER SEQRES 28 A 408 HIS GLY CYS LEU ASN VAL SER PRO SER ASN ALA GLN TRP SEQRES 29 A 408 PHE TYR ASP HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL SEQRES 30 A 408 VAL ASN THR VAL GLY GLY THR LEU PRO GLY ILE ASP GLY SEQRES 31 A 408 LEU GLY ASP TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA SEQRES 32 A 408 GLY ASN ALA LYS ALA SEQRES 1 B 408 MET PRO LYS VAL GLY ILE ALA ALA GLN ALA GLY ARG THR SEQRES 2 B 408 ARG VAL ARG ARG ALA TRP LEU THR ALA LEU MET MET THR SEQRES 3 B 408 ALA VAL MET ILE GLY ALA VAL ALA CYS GLY SER GLY ARG SEQRES 4 B 408 GLY PRO ALA PRO ILE LYS VAL ILE ALA ASP LYS GLY THR SEQRES 5 B 408 PRO PHE ALA ASP LEU LEU VAL PRO LYS LEU THR ALA SER SEQRES 6 B 408 VAL THR ASP GLY ALA VAL GLY VAL THR VAL ASP ALA PRO SEQRES 7 B 408 VAL SER VAL THR ALA ALA ASP GLY VAL LEU ALA ALA VAL SEQRES 8 B 408 THR MET VAL ASN ASP ASN GLY ARG PRO VAL ALA GLY ARG SEQRES 9 B 408 LEU SER PRO ASP GLY LEU ARG TRP SER THR THR GLU GLN SEQRES 10 B 408 LEU GLY TYR ASN ARG ARG TYR THR LEU ASN ALA THR ALA SEQRES 11 B 408 LEU GLY LEU GLY GLY ALA ALA THR ARG GLN LEU THR PHE SEQRES 12 B 408 GLN THR SER SER PRO ALA HIS LEU THR MET PRO TYR VAL SEQRES 13 B 408 MET PRO GLY ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO SEQRES 14 B 408 VAL ALA ILE ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY SEQRES 15 B 408 ALA ALA GLU LYS ALA ILE LYS ILE THR THR ASN PRO PRO SEQRES 16 B 408 VAL GLU GLY ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL SEQRES 17 B 408 ARG TRP ARG PRO GLU HIS PHE TRP LYS PRO GLY THR ALA SEQRES 18 B 408 VAL ASP VAL ALA VAL ASN THR TYR GLY VAL ASP LEU GLY SEQRES 19 B 408 GLU GLY MET PHE GLY GLU ASP ASN VAL GLN THR HIS PHE SEQRES 20 B 408 THR ILE GLY ASP GLU VAL ILE ALA THR ALA ASP ASP ASN SEQRES 21 B 408 THR LYS ILE LEU THR VAL ARG VAL ASN GLY GLU VAL VAL SEQRES 22 B 408 LYS SER MET PRO THR SER MET GLY LYS ASP SER THR PRO SEQRES 23 B 408 THR ALA ASN GLY ILE TYR ILE VAL GLY SER ARG TYR LYS SEQRES 24 B 408 HIS ILE ILE MET ASP SER SER THR TYR GLY VAL PRO VAL SEQRES 25 B 408 ASN SER PRO ASN GLY TYR ARG THR ASP VAL ASP TRP ALA SEQRES 26 B 408 THR GLN ILE SER TYR SER GLY VAL PHE VAL HIS SER ALA SEQRES 27 B 408 PRO TRP SER VAL GLY ALA GLN GLY HIS THR ASN THR SER SEQRES 28 B 408 HIS GLY CYS LEU ASN VAL SER PRO SER ASN ALA GLN TRP SEQRES 29 B 408 PHE TYR ASP HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL SEQRES 30 B 408 VAL ASN THR VAL GLY GLY THR LEU PRO GLY ILE ASP GLY SEQRES 31 B 408 LEU GLY ASP TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA SEQRES 32 B 408 GLY ASN ALA LYS ALA HET GOL A 501 6 HET GOL A 502 6 HET 6QR A 503 25 HET GOL B 501 6 HET 6QR B 502 25 HETNAM GOL GLYCEROL HETNAM 6QR (2~{S},3~{R},4~{R})-4-(1~{H}-INDOL-3-YLSULFANYL)-3- HETNAM 2 6QR METHYL-2-[(2~{S},3~{S})-3-OXIDANYL-1-OXIDANYLIDENE- HETNAM 3 6QR BUTAN-2-YL]-3,4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLIC HETNAM 4 6QR ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 3(C3 H8 O3) FORMUL 5 6QR 2(C18 H20 N2 O4 S) FORMUL 8 HOH *284(H2 O) HELIX 1 AA1 ASP A 180 ALA A 187 1 8 HELIX 2 AA2 SER A 306 GLY A 309 5 4 HELIX 3 AA3 PRO A 339 VAL A 342 5 4 HELIX 4 AA4 SER A 358 VAL A 369 1 12 HELIX 5 AA5 GLY A 392 ILE A 396 5 5 HELIX 6 AA6 PRO A 397 GLY A 404 1 8 HELIX 7 AA7 ASP B 180 ALA B 187 1 8 HELIX 8 AA8 SER B 306 GLY B 309 5 4 HELIX 9 AA9 PRO B 339 VAL B 342 5 4 HELIX 10 AB1 SER B 358 VAL B 369 1 12 HELIX 11 AB2 GLY B 392 ILE B 396 5 5 HELIX 12 AB3 PRO B 397 GLY B 404 1 8 SHEET 1 AA1 4 LYS A 61 ALA A 64 0 SHEET 2 AA1 4 SER A 80 ALA A 84 -1 O ALA A 84 N LYS A 61 SHEET 3 AA1 4 ARG A 111 THR A 114 -1 O TRP A 112 N VAL A 81 SHEET 4 AA1 4 GLY A 103 LEU A 105 -1 N ARG A 104 O SER A 113 SHEET 1 AA2 3 VAL A 87 VAL A 94 0 SHEET 2 AA2 3 ARG A 123 GLY A 132 -1 O ASN A 127 N THR A 92 SHEET 3 AA2 3 GLY A 135 GLN A 144 -1 O LEU A 141 N LEU A 126 SHEET 1 AA3 2 HIS A 150 THR A 152 0 SHEET 2 AA3 2 MET A 237 GLY A 239 1 O PHE A 238 N HIS A 150 SHEET 1 AA4 4 PRO A 154 MET A 157 0 SHEET 2 AA4 4 VAL A 170 PHE A 174 -1 O ARG A 173 N TYR A 155 SHEET 3 AA4 4 GLU A 207 PRO A 212 -1 O VAL A 208 N ILE A 172 SHEET 4 AA4 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 AA5 4 GLU A 162 VAL A 164 0 SHEET 2 AA5 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 AA5 4 ALA A 221 VAL A 226 -1 N VAL A 226 O VAL A 243 SHEET 4 AA5 4 ILE A 188 ASN A 193 -1 N ASN A 193 O ALA A 221 SHEET 1 AA6 5 GLU A 271 PRO A 277 0 SHEET 2 AA6 5 ILE A 263 VAL A 268 -1 N LEU A 264 O MET A 276 SHEET 3 AA6 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 AA6 5 ILE A 374 VAL A 378 1 O GLU A 376 N ALA A 257 SHEET 5 AA6 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 AA7 4 ARG A 297 ASP A 304 0 SHEET 2 AA7 4 ARG A 319 GLN A 327 -1 O THR A 320 N MET A 303 SHEET 3 AA7 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 AA7 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 AA8 4 LYS B 61 ALA B 64 0 SHEET 2 AA8 4 SER B 80 ALA B 84 -1 O THR B 82 N THR B 63 SHEET 3 AA8 4 ARG B 111 THR B 114 -1 O TRP B 112 N VAL B 81 SHEET 4 AA8 4 GLY B 103 LEU B 105 -1 N ARG B 104 O SER B 113 SHEET 1 AA9 3 VAL B 87 VAL B 94 0 SHEET 2 AA9 3 ARG B 123 GLY B 132 -1 O ASN B 127 N THR B 92 SHEET 3 AA9 3 GLY B 135 GLN B 144 -1 O LEU B 141 N LEU B 126 SHEET 1 AB1 2 HIS B 150 THR B 152 0 SHEET 2 AB1 2 MET B 237 GLY B 239 1 O PHE B 238 N HIS B 150 SHEET 1 AB2 4 PRO B 154 MET B 157 0 SHEET 2 AB2 4 VAL B 170 PHE B 174 -1 O ARG B 173 N TYR B 155 SHEET 3 AB2 4 GLU B 207 PRO B 212 -1 O TRP B 210 N VAL B 170 SHEET 4 AB2 4 GLY B 198 TRP B 202 -1 N TYR B 201 O ARG B 209 SHEET 1 AB3 4 VAL B 163 VAL B 164 0 SHEET 2 AB3 4 VAL B 243 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 AB3 4 ALA B 221 VAL B 226 -1 N VAL B 224 O THR B 245 SHEET 4 AB3 4 ILE B 188 ASN B 193 -1 N LYS B 189 O ALA B 225 SHEET 1 AB4 5 GLU B 271 PRO B 277 0 SHEET 2 AB4 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 AB4 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 AB4 5 ILE B 374 VAL B 378 1 O GLU B 376 N ALA B 257 SHEET 5 AB4 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 AB5 4 ARG B 297 ASP B 304 0 SHEET 2 AB5 4 ARG B 319 GLN B 327 -1 O TRP B 324 N LYS B 299 SHEET 3 AB5 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 AB5 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK SG CYS A 354 C1 6QR A 503 1555 1555 1.82 LINK SG CYS B 354 C1 6QR B 502 1555 1555 1.96 CISPEP 1 MET A 157 PRO A 158 0 0.08 CISPEP 2 ASN A 193 PRO A 194 0 -0.50 CISPEP 3 MET B 157 PRO B 158 0 0.92 CISPEP 4 ASN B 193 PRO B 194 0 2.28 SITE 1 AC1 5 GLU A 213 HIS A 214 PHE A 215 ILE A 291 SITE 2 AC1 5 TRP A 394 SITE 1 AC2 7 ILE A 188 LYS A 189 ILE A 190 GLY A 198 SITE 2 AC2 7 PHE A 200 TRP A 210 HOH A 608 SITE 1 AC3 13 MET A 303 TYR A 318 THR A 320 GLY A 332 SITE 2 AC3 13 HIS A 336 TRP A 340 SER A 351 HIS A 352 SITE 3 AC3 13 GLY A 353 CYS A 354 ASN A 356 HOH A 665 SITE 4 AC3 13 HOH A 694 SITE 1 AC4 4 GLU B 213 HIS B 214 PHE B 215 ILE B 291 SITE 1 AC5 15 SER B 279 MET B 280 MET B 303 TYR B 318 SITE 2 AC5 15 GLY B 332 PHE B 334 HIS B 336 TRP B 340 SITE 3 AC5 15 SER B 351 HIS B 352 GLY B 353 LEU B 355 SITE 4 AC5 15 ASN B 356 HOH B 605 HOH B 727 CRYST1 61.140 94.150 75.630 90.00 93.20 90.00 P 1 21 1 4 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 0.016356 0.000000 0.000914 0.00000 SCALE2 0.000000 0.010621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013243 0.00000