HEADER BIOSYNTHETIC PROTEIN 14-JAN-19 6NNC
TITLE STRUCTURE OF DIHYDROFOLATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS
TITLE 2 IN COMPLEX WITH NADPH AND PEMETREXED
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 1.5.1.3;
COMPND 5 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: FOLA, DFRA, RV2763C, MTV002.28C;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ANTIFOLATE, BIOSYNTHETIC PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.A.RIBEIRO,S.M.CHAVEZ-PACHECO,M.V.B.DIAS
REVDAT 3 13-MAR-24 6NNC 1 LINK
REVDAT 2 13-NOV-19 6NNC 1 JRNL
REVDAT 1 17-JUL-19 6NNC 0
JRNL AUTH J.A.RIBEIRO,S.M.CHAVEZ-PACHECO,G.S.DE OLIVEIRA,C.D.S.SILVA,
JRNL AUTH 2 J.H.P.GIUDICE,G.A.LIBREROS-ZUNIGA,M.V.B.DIAS
JRNL TITL CRYSTAL STRUCTURES OF THE CLOSED FORM OF MYCOBACTERIUM
JRNL TITL 2 TUBERCULOSIS DIHYDROFOLATE REDUCTASE IN COMPLEX WITH
JRNL TITL 3 DIHYDROFOLATE AND ANTIFOLATES.
JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 682 2019
JRNL REF 2 BIOL
JRNL REFN ISSN 2059-7983
JRNL PMID 31282477
JRNL DOI 10.1107/S205979831900901X
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.14_3260)
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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.16
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 3 NUMBER OF REFLECTIONS : 29234
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.163
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.204
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080
REMARK 3 FREE R VALUE TEST SET COUNT : 1485
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 32.1637 - 4.0009 0.99 2736 138 0.1513 0.1935
REMARK 3 2 4.0009 - 3.1765 1.00 2599 149 0.1496 0.1896
REMARK 3 3 3.1765 - 2.7752 1.00 2588 133 0.1623 0.2136
REMARK 3 4 2.7752 - 2.5216 1.00 2554 139 0.1668 0.2040
REMARK 3 5 2.5216 - 2.3409 0.99 2535 140 0.1611 0.1952
REMARK 3 6 2.3409 - 2.2029 0.99 2524 120 0.1634 0.2046
REMARK 3 7 2.2029 - 2.0926 0.99 2521 142 0.1684 0.2080
REMARK 3 8 2.0926 - 2.0016 0.98 2499 126 0.1765 0.2397
REMARK 3 9 2.0016 - 1.9245 0.98 2476 154 0.1694 0.2301
REMARK 3 10 1.9245 - 1.8581 0.96 2380 130 0.1711 0.2127
REMARK 3 11 1.8581 - 1.8000 0.92 2337 114 0.1838 0.2366
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) : 0.160
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.360
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 18.87
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.16
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 22.9291 0.1282 17.7536
REMARK 3 T TENSOR
REMARK 3 T11: 0.1444 T22: 0.1238
REMARK 3 T33: 0.1161 T12: -0.0093
REMARK 3 T13: -0.0296 T23: -0.0103
REMARK 3 L TENSOR
REMARK 3 L11: 1.1986 L22: 0.4743
REMARK 3 L33: 0.2465 L12: -0.4486
REMARK 3 L13: -0.4724 L23: 0.0551
REMARK 3 S TENSOR
REMARK 3 S11: 0.0024 S12: -0.0102 S13: 0.0593
REMARK 3 S21: -0.0118 S22: -0.0063 S23: -0.0711
REMARK 3 S31: -0.0065 S32: 0.0114 S33: 0.0011
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : 1
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 1 THROUGH 154 OR
REMARK 3 RESID 156 THROUGH 159))
REMARK 3 SELECTION : (CHAIN B AND (RESID 1 THROUGH 154 OR
REMARK 3 RESID 156 THROUGH 159))
REMARK 3 ATOM PAIRS NUMBER : 972
REMARK 3 RMSD : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6NNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-19.
REMARK 100 THE DEPOSITION ID IS D_1000239007.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-APR-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : LNLS
REMARK 200 BEAMLINE : W01B-MX2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.4
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29295
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 46.750
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 12.60
REMARK 200 R MERGE (I) : 0.06600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84
REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6
REMARK 200 DATA REDUNDANCY IN SHELL : 11.00
REMARK 200 R MERGE FOR SHELL (I) : 0.41700
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.53
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULPHATE, 100 MM MES,
REMARK 280 10 MM COBALT CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
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 30.67300
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.10800
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.35900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.10800
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.67300
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.35900
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, 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 7270 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14380 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 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 NH2 ARG B 143 O HOH B 301 1.98
REMARK 500 O HOH B 387 O HOH B 448 2.07
REMARK 500 OG SER B 159 O HOH B 302 2.13
REMARK 500 O HOH B 403 O HOH B 439 2.13
REMARK 500 O HOH B 376 O HOH B 377 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 427 O HOH B 441 2555 2.08
REMARK 500 OD1 ASP B 70 O HOH B 406 2654 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 MET B 72 CA - CB - CG ANGL. DEV. = 15.6 DEGREES
REMARK 500 MET B 72 CB - CG - SD ANGL. DEV. = -25.2 DEGREES
REMARK 500 LEU B 102 CB - CG - CD2 ANGL. DEV. = -16.6 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASP A 19 -159.16 -140.42
REMARK 500 PRO A 21 38.19 -88.17
REMARK 500 LEU A 86 59.46 -98.29
REMARK 500 ASP A 132 -161.48 -78.11
REMARK 500 PRO B 21 42.57 -85.80
REMARK 500 LEU B 86 66.43 -100.18
REMARK 500 ASP B 132 -163.95 -75.39
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 CO A 202 CO
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 38 NE2
REMARK 620 2 HOH A 327 O 92.7
REMARK 620 3 HOH A 345 O 89.2 84.3
REMARK 620 4 HOH A 346 O 89.5 177.7 95.0
REMARK 620 5 HIS B 157 NE2 173.1 94.0 90.0 83.7
REMARK 620 6 HOH B 391 O 92.5 92.9 176.9 87.7 88.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CO B 202 CO
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 383 O
REMARK 620 2 HIS B 38 NE2 173.7
REMARK 620 3 HOH B 309 O 81.7 92.8
REMARK 620 4 HOH B 335 O 92.7 89.8 84.2
REMARK 620 5 HOH B 344 O 86.1 91.4 94.9 178.6
REMARK 620 6 HOH B 395 O 96.9 88.8 175.1 91.2 89.7
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 NDP A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue LYA A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NDP B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CO B 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue LYA B 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 205
DBREF 6NNC A 1 159 UNP P9WNX1 DYR_MYCTU 3 161
DBREF 6NNC B 1 159 UNP P9WNX1 DYR_MYCTU 3 161
SEQRES 1 A 159 MET VAL GLY LEU ILE TRP ALA GLN ALA THR SER GLY VAL
SEQRES 2 A 159 ILE GLY ARG GLY GLY ASP ILE PRO TRP ARG LEU PRO GLU
SEQRES 3 A 159 ASP GLN ALA HIS PHE ARG GLU ILE THR MET GLY HIS THR
SEQRES 4 A 159 ILE VAL MET GLY ARG ARG THR TRP ASP SER LEU PRO ALA
SEQRES 5 A 159 LYS VAL ARG PRO LEU PRO GLY ARG ARG ASN VAL VAL LEU
SEQRES 6 A 159 SER ARG GLN ALA ASP PHE MET ALA SER GLY ALA GLU VAL
SEQRES 7 A 159 VAL GLY SER LEU GLU GLU ALA LEU THR SER PRO GLU THR
SEQRES 8 A 159 TRP VAL ILE GLY GLY GLY GLN VAL TYR ALA LEU ALA LEU
SEQRES 9 A 159 PRO TYR ALA THR ARG CYS GLU VAL THR GLU VAL ASP ILE
SEQRES 10 A 159 GLY LEU PRO ARG GLU ALA GLY ASP ALA LEU ALA PRO VAL
SEQRES 11 A 159 LEU ASP GLU THR TRP ARG GLY GLU THR GLY GLU TRP ARG
SEQRES 12 A 159 PHE SER ARG SER GLY LEU ARG TYR ARG LEU TYR SER TYR
SEQRES 13 A 159 HIS ARG SER
SEQRES 1 B 159 MET VAL GLY LEU ILE TRP ALA GLN ALA THR SER GLY VAL
SEQRES 2 B 159 ILE GLY ARG GLY GLY ASP ILE PRO TRP ARG LEU PRO GLU
SEQRES 3 B 159 ASP GLN ALA HIS PHE ARG GLU ILE THR MET GLY HIS THR
SEQRES 4 B 159 ILE VAL MET GLY ARG ARG THR TRP ASP SER LEU PRO ALA
SEQRES 5 B 159 LYS VAL ARG PRO LEU PRO GLY ARG ARG ASN VAL VAL LEU
SEQRES 6 B 159 SER ARG GLN ALA ASP PHE MET ALA SER GLY ALA GLU VAL
SEQRES 7 B 159 VAL GLY SER LEU GLU GLU ALA LEU THR SER PRO GLU THR
SEQRES 8 B 159 TRP VAL ILE GLY GLY GLY GLN VAL TYR ALA LEU ALA LEU
SEQRES 9 B 159 PRO TYR ALA THR ARG CYS GLU VAL THR GLU VAL ASP ILE
SEQRES 10 B 159 GLY LEU PRO ARG GLU ALA GLY ASP ALA LEU ALA PRO VAL
SEQRES 11 B 159 LEU ASP GLU THR TRP ARG GLY GLU THR GLY GLU TRP ARG
SEQRES 12 B 159 PHE SER ARG SER GLY LEU ARG TYR ARG LEU TYR SER TYR
SEQRES 13 B 159 HIS ARG SER
HET NDP A 201 48
HET CO A 202 1
HET LYA A 203 31
HET SO4 A 204 5
HET SO4 A 205 5
HET NDP B 201 48
HET CO B 202 1
HET LYA B 203 31
HET SO4 B 204 5
HET SO4 B 205 5
HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM 2 NDP PHOSPHATE
HETNAM CO COBALT (II) ION
HETNAM LYA 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-
HETNAM 2 LYA D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC
HETNAM 3 LYA ACID
HETNAM SO4 SULFATE ION
HETSYN LYA LY231514
FORMUL 3 NDP 2(C21 H30 N7 O17 P3)
FORMUL 4 CO 2(CO 2+)
FORMUL 5 LYA 2(C20 H21 N5 O6)
FORMUL 6 SO4 4(O4 S 2-)
FORMUL 13 HOH *316(H2 O)
HELIX 1 AA1 LEU A 24 MET A 36 1 13
HELIX 2 AA2 ARG A 44 LEU A 50 1 7
HELIX 3 AA3 PRO A 51 ARG A 55 5 5
HELIX 4 AA4 SER A 81 LEU A 86 5 6
HELIX 5 AA5 GLY A 96 LEU A 104 1 9
HELIX 6 AA6 PRO A 105 ALA A 107 5 3
HELIX 7 AA7 LEU B 24 MET B 36 1 13
HELIX 8 AA8 ARG B 44 LEU B 50 1 7
HELIX 9 AA9 PRO B 51 ARG B 55 5 5
HELIX 10 AB1 SER B 81 LEU B 86 1 6
HELIX 11 AB2 GLY B 96 LEU B 104 1 9
HELIX 12 AB3 PRO B 105 ALA B 107 5 3
SHEET 1 AA1 8 GLU A 77 VAL A 79 0
SHEET 2 AA1 8 ARG A 61 LEU A 65 1 N VAL A 64 O GLU A 77
SHEET 3 AA1 8 THR A 39 GLY A 43 1 N ILE A 40 O VAL A 63
SHEET 4 AA1 8 THR A 91 VAL A 93 1 O TRP A 92 N THR A 39
SHEET 5 AA1 8 VAL A 2 ALA A 9 1 N GLY A 3 O VAL A 93
SHEET 6 AA1 8 ARG A 109 VAL A 115 1 O VAL A 115 N GLN A 8
SHEET 7 AA1 8 ARG A 150 HIS A 157 -1 O TYR A 154 N VAL A 112
SHEET 8 AA1 8 ARG A 136 THR A 139 -1 N ARG A 136 O HIS A 157
SHEET 1 AA2 8 GLU A 77 VAL A 79 0
SHEET 2 AA2 8 ARG A 61 LEU A 65 1 N VAL A 64 O GLU A 77
SHEET 3 AA2 8 THR A 39 GLY A 43 1 N ILE A 40 O VAL A 63
SHEET 4 AA2 8 THR A 91 VAL A 93 1 O TRP A 92 N THR A 39
SHEET 5 AA2 8 VAL A 2 ALA A 9 1 N GLY A 3 O VAL A 93
SHEET 6 AA2 8 ARG A 109 VAL A 115 1 O VAL A 115 N GLN A 8
SHEET 7 AA2 8 ARG A 150 HIS A 157 -1 O TYR A 154 N VAL A 112
SHEET 8 AA2 8 ARG A 143 PHE A 144 -1 N ARG A 143 O TYR A 151
SHEET 1 AA3 2 VAL A 13 GLY A 15 0
SHEET 2 AA3 2 ALA A 126 LEU A 127 -1 O ALA A 126 N ILE A 14
SHEET 1 AA4 8 GLU B 77 VAL B 79 0
SHEET 2 AA4 8 ARG B 61 LEU B 65 1 N VAL B 64 O GLU B 77
SHEET 3 AA4 8 THR B 39 GLY B 43 1 N MET B 42 O LEU B 65
SHEET 4 AA4 8 THR B 91 VAL B 93 1 O TRP B 92 N THR B 39
SHEET 5 AA4 8 VAL B 2 ALA B 9 1 N GLY B 3 O VAL B 93
SHEET 6 AA4 8 ARG B 109 VAL B 115 1 O THR B 113 N GLN B 8
SHEET 7 AA4 8 ARG B 150 HIS B 157 -1 O TYR B 154 N VAL B 112
SHEET 8 AA4 8 ARG B 136 THR B 139 -1 N ARG B 136 O HIS B 157
SHEET 1 AA5 8 GLU B 77 VAL B 79 0
SHEET 2 AA5 8 ARG B 61 LEU B 65 1 N VAL B 64 O GLU B 77
SHEET 3 AA5 8 THR B 39 GLY B 43 1 N MET B 42 O LEU B 65
SHEET 4 AA5 8 THR B 91 VAL B 93 1 O TRP B 92 N THR B 39
SHEET 5 AA5 8 VAL B 2 ALA B 9 1 N GLY B 3 O VAL B 93
SHEET 6 AA5 8 ARG B 109 VAL B 115 1 O THR B 113 N GLN B 8
SHEET 7 AA5 8 ARG B 150 HIS B 157 -1 O TYR B 154 N VAL B 112
SHEET 8 AA5 8 ARG B 143 PHE B 144 -1 N ARG B 143 O TYR B 151
SHEET 1 AA6 2 VAL B 13 GLY B 15 0
SHEET 2 AA6 2 ALA B 126 LEU B 127 -1 O ALA B 126 N ILE B 14
LINK NE2 HIS A 38 CO CO A 202 1555 1555 2.16
LINK CO CO A 202 O HOH A 327 1555 1555 2.18
LINK CO CO A 202 O HOH A 345 1555 1555 2.15
LINK CO CO A 202 O HOH A 346 1555 1555 2.19
LINK CO CO A 202 NE2 HIS B 157 1555 1555 2.08
LINK CO CO A 202 O HOH B 391 1555 1555 2.16
LINK O HOH A 383 CO CO B 202 1555 1555 2.03
LINK NE2 HIS B 38 CO CO B 202 1555 1555 2.17
LINK CO CO B 202 O HOH B 309 1555 1555 2.15
LINK CO CO B 202 O HOH B 335 1555 1555 2.19
LINK CO CO B 202 O HOH B 344 1555 1555 2.30
LINK CO CO B 202 O HOH B 395 1555 1555 2.10
CISPEP 1 ARG A 55 PRO A 56 0 0.14
CISPEP 2 GLY A 95 GLY A 96 0 6.04
CISPEP 3 ARG B 55 PRO B 56 0 1.66
CISPEP 4 GLY B 95 GLY B 96 0 5.29
SITE 1 AC1 35 TRP A 6 ALA A 7 ILE A 14 GLY A 15
SITE 2 AC1 35 ARG A 16 GLY A 18 ASP A 19 ILE A 20
SITE 3 AC1 35 GLY A 43 ARG A 44 ARG A 45 THR A 46
SITE 4 AC1 35 LEU A 65 SER A 66 ARG A 67 GLN A 68
SITE 5 AC1 35 GLY A 80 ILE A 94 GLY A 96 GLY A 97
SITE 6 AC1 35 GLN A 98 VAL A 99 TYR A 100 LEU A 102
SITE 7 AC1 35 ALA A 126 LYA A 203 HOH A 306 HOH A 318
SITE 8 AC1 35 HOH A 325 HOH A 337 HOH A 338 HOH A 351
SITE 9 AC1 35 HOH A 360 HOH A 379 HOH A 399
SITE 1 AC2 6 HIS A 38 HOH A 327 HOH A 345 HOH A 346
SITE 2 AC2 6 HIS B 157 HOH B 391
SITE 1 AC3 20 ILE A 5 TRP A 6 ALA A 7 ASP A 27
SITE 2 AC3 20 GLN A 28 PHE A 31 ARG A 32 LEU A 50
SITE 3 AC3 20 LEU A 57 ARG A 60 ILE A 94 TYR A 100
SITE 4 AC3 20 THR A 113 NDP A 201 HOH A 324 HOH A 350
SITE 5 AC3 20 HOH A 362 HOH A 393 HOH A 401 HOH A 411
SITE 1 AC4 6 ARG A 23 PRO A 51 HOH A 309 HOH A 367
SITE 2 AC4 6 ARG B 32 PRO B 58
SITE 1 AC5 2 ARG A 44 ARG A 45
SITE 1 AC6 33 TRP B 6 ALA B 7 ILE B 14 GLY B 15
SITE 2 AC6 33 ARG B 16 GLY B 18 ASP B 19 ILE B 20
SITE 3 AC6 33 GLY B 43 ARG B 44 ARG B 45 THR B 46
SITE 4 AC6 33 LEU B 65 SER B 66 ARG B 67 GLN B 68
SITE 5 AC6 33 GLY B 80 ILE B 94 GLY B 96 GLY B 97
SITE 6 AC6 33 GLN B 98 VAL B 99 TYR B 100 LEU B 102
SITE 7 AC6 33 LYA B 203 HOH B 321 HOH B 322 HOH B 331
SITE 8 AC6 33 HOH B 333 HOH B 358 HOH B 372 HOH B 382
SITE 9 AC6 33 HOH B 389
SITE 1 AC7 6 HOH A 383 HIS B 38 HOH B 309 HOH B 335
SITE 2 AC7 6 HOH B 344 HOH B 395
SITE 1 AC8 21 ILE B 5 TRP B 6 ALA B 7 ASP B 27
SITE 2 AC8 21 GLN B 28 ALA B 29 PHE B 31 ARG B 32
SITE 3 AC8 21 LEU B 50 VAL B 54 ARG B 60 ILE B 94
SITE 4 AC8 21 TYR B 100 NDP B 201 HOH B 304 HOH B 307
SITE 5 AC8 21 HOH B 310 HOH B 311 HOH B 355 HOH B 369
SITE 6 AC8 21 HOH B 371
SITE 1 AC9 3 ARG B 44 ARG B 45 HOH B 394
SITE 1 AD1 4 ARG A 136 HOH A 304 ALA B 29 ARG B 146
CRYST1 61.346 70.718 72.216 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 0.016301 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014141 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013847 0.00000