HEADER REPLICATION 24-MAR-19 6R4U
TITLE CRYSTAL STRUCTURE OF THE PRI1 SUBUNIT OF HUMAN PRIMASE BOUND TO
TITLE 2 FLUDARABINE TRIPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA PRIMASE SMALL SUBUNIT;
COMPND 3 CHAIN: A, E;
COMPND 4 SYNONYM: DNA PRIMASE 49 KDA SUBUNIT,P49;
COMPND 5 EC: 2.7.7.-;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PRIM1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2
KEYWDS PRIMASE, DNA-DEPENDENT RNA POLYMERASE, ATP, PRIMING, REPLICATION
EXPDTA X-RAY DIFFRACTION
AUTHOR M.L.KILKENNY,L.PELLEGRINI
REVDAT 3 24-JAN-24 6R4U 1 COMPND HETNAM LINK
REVDAT 2 02-OCT-19 6R4U 1 JRNL
REVDAT 1 11-SEP-19 6R4U 0
JRNL AUTH S.HOLZER,N.J.RZECHORZEK,I.R.SHORT,M.JENKYN-BEDFORD,
JRNL AUTH 2 L.PELLEGRINI,M.L.KILKENNY
JRNL TITL STRUCTURAL BASIS FOR INHIBITION OF HUMAN PRIMASE BY
JRNL TITL 2 ARABINOFURANOSYL NUCLEOSIDE ANALOGUES FLUDARABINE AND
JRNL TITL 3 VIDARABINE.
JRNL REF ACS CHEM.BIOL. V. 14 1904 2019
JRNL REFN ESSN 1554-8937
JRNL PMID 31479243
JRNL DOI 10.1021/ACSCHEMBIO.9B00367
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.14_3260_000
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.13
REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1
REMARK 3 NUMBER OF REFLECTIONS : 48326
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.198
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.223
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010
REMARK 3 FREE R VALUE TEST SET COUNT : 2419
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : NULL
REMARK 3 SHRINKAGE RADIUS : NULL
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL
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 : 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 : 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 6R4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-19.
REMARK 100 THE DEPOSITION ID IS D_1292100925.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-NOV-14
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 : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97944
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49380
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 46.125
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 6.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.9100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.520
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: 6RB4
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG3350, 10% ETHYLENE GLYCOL, 200
REMARK 280 MM NA/K TARTRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.40000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.40000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 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 55.41500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.78500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.41500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.78500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.40000
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.41500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.78500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.40000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.41500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.78500
REMARK 290 SMTRY3 8 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 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: E
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A -2
REMARK 465 THR A -1
REMARK 465 SER A 0
REMARK 465 MET A 1
REMARK 465 GLU A 2
REMARK 465 THR A 3
REMARK 465 PHE A 4
REMARK 465 ASP A 5
REMARK 465 SER A 361
REMARK 465 THR A 362
REMARK 465 ASN A 363
REMARK 465 GLU A 364
REMARK 465 GLU A 365
REMARK 465 GLU A 366
REMARK 465 LYS A 367
REMARK 465 GLU A 368
REMARK 465 GLU A 369
REMARK 465 ASN A 370
REMARK 465 GLU A 371
REMARK 465 ALA A 372
REMARK 465 GLU A 373
REMARK 465 SER A 374
REMARK 465 ASP A 375
REMARK 465 VAL A 376
REMARK 465 LYS A 377
REMARK 465 HIS A 378
REMARK 465 ARG A 379
REMARK 465 THR A 380
REMARK 465 GLY E -2
REMARK 465 THR E -1
REMARK 465 SER E 0
REMARK 465 MET E 1
REMARK 465 GLU E 2
REMARK 465 THR E 3
REMARK 465 ILE E 360
REMARK 465 SER E 361
REMARK 465 THR E 362
REMARK 465 ASN E 363
REMARK 465 GLU E 364
REMARK 465 GLU E 365
REMARK 465 GLU E 366
REMARK 465 LYS E 367
REMARK 465 GLU E 368
REMARK 465 GLU E 369
REMARK 465 ASN E 370
REMARK 465 GLU E 371
REMARK 465 ALA E 372
REMARK 465 GLU E 373
REMARK 465 SER E 374
REMARK 465 ASP E 375
REMARK 465 VAL E 376
REMARK 465 LYS E 377
REMARK 465 HIS E 378
REMARK 465 ARG E 379
REMARK 465 THR E 380
REMARK 465 ARG E 381
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 LEU A 49 -155.93 -101.16
REMARK 500 SER A 124 -132.01 58.34
REMARK 500 ARG A 162 -63.85 -140.31
REMARK 500 VAL A 229 -70.96 -115.57
REMARK 500 ASP A 286 42.34 -109.94
REMARK 500 LEU E 49 -155.45 -100.41
REMARK 500 LYS E 104 146.98 -170.64
REMARK 500 SER E 124 -133.60 58.51
REMARK 500 ARG E 162 -65.35 -138.96
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 MN A 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 109 OD1
REMARK 620 2 ASP A 111 OD1 95.3
REMARK 620 3 HFD A 504 O2A 109.4 102.2
REMARK 620 4 HFD A 504 O2B 88.5 173.8 81.1
REMARK 620 5 HFD A 504 O2G 161.9 90.8 85.8 84.2
REMARK 620 6 HOH A 635 O 75.5 88.6 167.4 87.6 87.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 503 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 109 OD2
REMARK 620 2 ASP A 111 OD2 100.8
REMARK 620 3 ASP A 306 OD2 97.2 100.1
REMARK 620 4 HFD A 504 O2A 77.7 93.4 166.2
REMARK 620 5 HOH A 662 O 168.9 88.6 86.7 96.1
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 501 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 121 SG
REMARK 620 2 CYS A 122 SG 119.1
REMARK 620 3 CYS A 128 SG 105.1 99.9
REMARK 620 4 CYS A 131 SG 104.1 112.4 116.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN E 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP E 109 OD1
REMARK 620 2 ASP E 111 OD1 95.4
REMARK 620 3 HFD E 504 O2A 111.1 99.5
REMARK 620 4 HFD E 504 O2B 91.2 170.6 84.2
REMARK 620 5 HFD E 504 O2G 166.0 88.1 81.6 83.9
REMARK 620 6 HOH E 629 O 73.1 80.2 175.7 95.4 94.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN E 503 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP E 109 OD2
REMARK 620 2 ASP E 111 OD2 103.4
REMARK 620 3 ASP E 306 OD2 99.7 96.8
REMARK 620 4 HFD E 504 O2A 82.1 87.4 174.8
REMARK 620 5 HOH E 638 O 161.1 85.5 95.7 81.7
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN E 501 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS E 121 SG
REMARK 620 2 CYS E 122 SG 120.7
REMARK 620 3 CYS E 128 SG 102.2 98.6
REMARK 620 4 CYS E 131 SG 106.3 114.3 114.1
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HFD A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN E 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN E 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HFD E 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 505
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6R4S RELATED DB: PDB
REMARK 900 RELATED ID: 6R4T RELATED DB: PDB
DBREF 6R4U A 1 407 UNP P49642 PRI1_HUMAN 1 407
DBREF 6R4U E 1 407 UNP P49642 PRI1_HUMAN 1 407
SEQADV 6R4U GLY A -2 UNP P49642 EXPRESSION TAG
SEQADV 6R4U THR A -1 UNP P49642 EXPRESSION TAG
SEQADV 6R4U SER A 0 UNP P49642 EXPRESSION TAG
SEQADV 6R4U GLY E -2 UNP P49642 EXPRESSION TAG
SEQADV 6R4U THR E -1 UNP P49642 EXPRESSION TAG
SEQADV 6R4U SER E 0 UNP P49642 EXPRESSION TAG
SEQRES 1 A 410 GLY THR SER MET GLU THR PHE ASP PRO THR GLU LEU PRO
SEQRES 2 A 410 GLU LEU LEU LYS LEU TYR TYR ARG ARG LEU PHE PRO TYR
SEQRES 3 A 410 SER GLN TYR TYR ARG TRP LEU ASN TYR GLY GLY VAL ILE
SEQRES 4 A 410 LYS ASN TYR PHE GLN HIS ARG GLU PHE SER PHE THR LEU
SEQRES 5 A 410 LYS ASP ASP ILE TYR ILE ARG TYR GLN SER PHE ASN ASN
SEQRES 6 A 410 GLN SER ASP LEU GLU LYS GLU MET GLN LYS MET ASN PRO
SEQRES 7 A 410 TYR LYS ILE ASP ILE GLY ALA VAL TYR SER HIS ARG PRO
SEQRES 8 A 410 ASN GLN HIS ASN THR VAL LYS LEU GLY ALA PHE GLN ALA
SEQRES 9 A 410 GLN GLU LYS GLU LEU VAL PHE ASP ILE ASP MET THR ASP
SEQRES 10 A 410 TYR ASP ASP VAL ARG ARG CYS CYS SER SER ALA ASP ILE
SEQRES 11 A 410 CYS PRO LYS CYS TRP THR LEU MET THR MET ALA ILE ARG
SEQRES 12 A 410 ILE ILE ASP ARG ALA LEU LYS GLU ASP PHE GLY PHE LYS
SEQRES 13 A 410 HIS ARG LEU TRP VAL TYR SER GLY ARG ARG GLY VAL HIS
SEQRES 14 A 410 CYS TRP VAL CYS ASP GLU SER VAL ARG LYS LEU SER SER
SEQRES 15 A 410 ALA VAL ARG SER GLY ILE VAL GLU TYR LEU SER LEU VAL
SEQRES 16 A 410 LYS GLY GLY GLN ASP VAL LYS LYS LYS VAL HIS LEU SER
SEQRES 17 A 410 GLU LYS ILE HIS PRO PHE ILE ARG LYS SER ILE ASN ILE
SEQRES 18 A 410 ILE LYS LYS TYR PHE GLU GLU TYR ALA LEU VAL ASN GLN
SEQRES 19 A 410 ASP ILE LEU GLU ASN LYS GLU SER TRP ASP LYS ILE LEU
SEQRES 20 A 410 ALA LEU VAL PRO GLU THR ILE HIS ASP GLU LEU GLN GLN
SEQRES 21 A 410 SER PHE GLN LYS SER HIS ASN SER LEU GLN ARG TRP GLU
SEQRES 22 A 410 HIS LEU LYS LYS VAL ALA SER ARG TYR GLN ASN ASN ILE
SEQRES 23 A 410 LYS ASN ASP LYS TYR GLY PRO TRP LEU GLU TRP GLU ILE
SEQRES 24 A 410 MET LEU GLN TYR CYS PHE PRO ARG LEU ASP ILE ASN VAL
SEQRES 25 A 410 SER LYS GLY ILE ASN HIS LEU LEU LYS SER PRO PHE SER
SEQRES 26 A 410 VAL HIS PRO LYS THR GLY ARG ILE SER VAL PRO ILE ASP
SEQRES 27 A 410 LEU GLN LYS VAL ASP GLN PHE ASP PRO PHE THR VAL PRO
SEQRES 28 A 410 THR ILE SER PHE ILE CYS ARG GLU LEU ASP ALA ILE SER
SEQRES 29 A 410 THR ASN GLU GLU GLU LYS GLU GLU ASN GLU ALA GLU SER
SEQRES 30 A 410 ASP VAL LYS HIS ARG THR ARG ASP TYR LYS LYS THR SER
SEQRES 31 A 410 LEU ALA PRO TYR VAL LYS VAL PHE GLU HIS PHE LEU GLU
SEQRES 32 A 410 ASN LEU ASP LYS SER ARG LYS
SEQRES 1 E 410 GLY THR SER MET GLU THR PHE ASP PRO THR GLU LEU PRO
SEQRES 2 E 410 GLU LEU LEU LYS LEU TYR TYR ARG ARG LEU PHE PRO TYR
SEQRES 3 E 410 SER GLN TYR TYR ARG TRP LEU ASN TYR GLY GLY VAL ILE
SEQRES 4 E 410 LYS ASN TYR PHE GLN HIS ARG GLU PHE SER PHE THR LEU
SEQRES 5 E 410 LYS ASP ASP ILE TYR ILE ARG TYR GLN SER PHE ASN ASN
SEQRES 6 E 410 GLN SER ASP LEU GLU LYS GLU MET GLN LYS MET ASN PRO
SEQRES 7 E 410 TYR LYS ILE ASP ILE GLY ALA VAL TYR SER HIS ARG PRO
SEQRES 8 E 410 ASN GLN HIS ASN THR VAL LYS LEU GLY ALA PHE GLN ALA
SEQRES 9 E 410 GLN GLU LYS GLU LEU VAL PHE ASP ILE ASP MET THR ASP
SEQRES 10 E 410 TYR ASP ASP VAL ARG ARG CYS CYS SER SER ALA ASP ILE
SEQRES 11 E 410 CYS PRO LYS CYS TRP THR LEU MET THR MET ALA ILE ARG
SEQRES 12 E 410 ILE ILE ASP ARG ALA LEU LYS GLU ASP PHE GLY PHE LYS
SEQRES 13 E 410 HIS ARG LEU TRP VAL TYR SER GLY ARG ARG GLY VAL HIS
SEQRES 14 E 410 CYS TRP VAL CYS ASP GLU SER VAL ARG LYS LEU SER SER
SEQRES 15 E 410 ALA VAL ARG SER GLY ILE VAL GLU TYR LEU SER LEU VAL
SEQRES 16 E 410 LYS GLY GLY GLN ASP VAL LYS LYS LYS VAL HIS LEU SER
SEQRES 17 E 410 GLU LYS ILE HIS PRO PHE ILE ARG LYS SER ILE ASN ILE
SEQRES 18 E 410 ILE LYS LYS TYR PHE GLU GLU TYR ALA LEU VAL ASN GLN
SEQRES 19 E 410 ASP ILE LEU GLU ASN LYS GLU SER TRP ASP LYS ILE LEU
SEQRES 20 E 410 ALA LEU VAL PRO GLU THR ILE HIS ASP GLU LEU GLN GLN
SEQRES 21 E 410 SER PHE GLN LYS SER HIS ASN SER LEU GLN ARG TRP GLU
SEQRES 22 E 410 HIS LEU LYS LYS VAL ALA SER ARG TYR GLN ASN ASN ILE
SEQRES 23 E 410 LYS ASN ASP LYS TYR GLY PRO TRP LEU GLU TRP GLU ILE
SEQRES 24 E 410 MET LEU GLN TYR CYS PHE PRO ARG LEU ASP ILE ASN VAL
SEQRES 25 E 410 SER LYS GLY ILE ASN HIS LEU LEU LYS SER PRO PHE SER
SEQRES 26 E 410 VAL HIS PRO LYS THR GLY ARG ILE SER VAL PRO ILE ASP
SEQRES 27 E 410 LEU GLN LYS VAL ASP GLN PHE ASP PRO PHE THR VAL PRO
SEQRES 28 E 410 THR ILE SER PHE ILE CYS ARG GLU LEU ASP ALA ILE SER
SEQRES 29 E 410 THR ASN GLU GLU GLU LYS GLU GLU ASN GLU ALA GLU SER
SEQRES 30 E 410 ASP VAL LYS HIS ARG THR ARG ASP TYR LYS LYS THR SER
SEQRES 31 E 410 LEU ALA PRO TYR VAL LYS VAL PHE GLU HIS PHE LEU GLU
SEQRES 32 E 410 ASN LEU ASP LYS SER ARG LYS
HET ZN A 501 1
HET MN A 502 1
HET MN A 503 1
HET HFD A 504 43
HET ZN E 501 1
HET MN E 502 1
HET MN E 503 1
HET HFD E 504 43
HET EDO E 505 10
HETNAM ZN ZINC ION
HETNAM MN MANGANESE (II) ION
HETNAM HFD 2-FLUORO-9-{5-O-[(R)-HYDROXY{[(R)-
HETNAM 2 HFD HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-
HETNAM 3 HFD D-ARABINOFURANOSYL}-9H-PURIN-6-A MINE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN HFD FLUDARABINE-TRIPHOSPHATE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 ZN 2(ZN 2+)
FORMUL 4 MN 4(MN 2+)
FORMUL 6 HFD 2(C10 H15 F N5 O13 P3)
FORMUL 11 EDO C2 H6 O2
FORMUL 12 HOH *191(H2 O)
HELIX 1 AA1 GLU A 8 LEU A 20 1 13
HELIX 2 AA2 PRO A 22 TYR A 32 1 11
HELIX 3 AA3 GLY A 33 VAL A 35 5 3
HELIX 4 AA4 LYS A 50 ASP A 52 5 3
HELIX 5 AA5 ASN A 62 ASN A 74 1 13
HELIX 6 AA6 ARG A 87 HIS A 91 5 5
HELIX 7 AA7 THR A 113 ARG A 119 5 7
HELIX 8 AA8 TRP A 132 ASP A 149 1 18
HELIX 9 AA9 SER A 173 LEU A 177 5 5
HELIX 10 AB1 SER A 178 SER A 190 1 13
HELIX 11 AB2 HIS A 209 LEU A 228 1 20
HELIX 12 AB3 ASN A 236 ALA A 245 1 10
HELIX 13 AB4 LEU A 246 VAL A 247 5 2
HELIX 14 AB5 PRO A 248 THR A 250 5 3
HELIX 15 AB6 ILE A 251 SER A 262 1 12
HELIX 16 AB7 ASN A 264 SER A 277 1 14
HELIX 17 AB8 PRO A 290 PHE A 302 1 13
HELIX 18 AB9 ASP A 306 GLY A 312 1 7
HELIX 19 AC1 ASP A 335 PHE A 342 5 8
HELIX 20 AC2 THR A 349 ASP A 358 1 10
HELIX 21 AC3 ASP A 382 THR A 386 5 5
HELIX 22 AC4 LEU A 388 LYS A 407 1 20
HELIX 23 AC5 ASP E 5 THR E 7 5 3
HELIX 24 AC6 GLU E 8 LEU E 20 1 13
HELIX 25 AC7 PRO E 22 TYR E 32 1 11
HELIX 26 AC8 GLY E 33 VAL E 35 5 3
HELIX 27 AC9 LYS E 50 ASP E 52 5 3
HELIX 28 AD1 ASN E 62 ASN E 74 1 13
HELIX 29 AD2 ARG E 87 HIS E 91 5 5
HELIX 30 AD3 THR E 113 ARG E 119 5 7
HELIX 31 AD4 TRP E 132 ASP E 149 1 18
HELIX 32 AD5 ASP E 171 LYS E 176 1 6
HELIX 33 AD6 SER E 178 SER E 190 1 13
HELIX 34 AD7 HIS E 209 LEU E 228 1 20
HELIX 35 AD8 ASN E 236 ALA E 245 1 10
HELIX 36 AD9 LEU E 246 VAL E 247 5 2
HELIX 37 AE1 PRO E 248 THR E 250 5 3
HELIX 38 AE2 ILE E 251 SER E 262 1 12
HELIX 39 AE3 ASN E 264 SER E 277 1 14
HELIX 40 AE4 PRO E 290 PHE E 302 1 13
HELIX 41 AE5 ASP E 306 GLY E 312 1 7
HELIX 42 AE6 ASP E 335 PHE E 342 5 8
HELIX 43 AE7 ASP E 343 VAL E 347 5 5
HELIX 44 AE8 THR E 349 LEU E 357 1 9
HELIX 45 AE9 ASP E 358 ALA E 359 5 2
HELIX 46 AF1 ASP E 382 THR E 386 5 5
HELIX 47 AF2 LEU E 388 LYS E 407 1 20
SHEET 1 AA1 4 TYR A 54 GLN A 58 0
SHEET 2 AA1 4 ARG A 43 THR A 48 -1 N PHE A 45 O GLN A 58
SHEET 3 AA1 4 LYS A 77 TYR A 84 -1 O ASP A 79 N SER A 46
SHEET 4 AA1 4 ALA A 101 GLU A 103 -1 O GLU A 103 N VAL A 83
SHEET 1 AA2 4 TYR A 54 GLN A 58 0
SHEET 2 AA2 4 ARG A 43 THR A 48 -1 N PHE A 45 O GLN A 58
SHEET 3 AA2 4 LYS A 77 TYR A 84 -1 O ASP A 79 N SER A 46
SHEET 4 AA2 4 LEU A 317 LYS A 318 -1 O LEU A 317 N ILE A 80
SHEET 1 AA3 3 LEU A 106 ASP A 111 0
SHEET 2 AA3 3 GLY A 164 VAL A 169 -1 O VAL A 169 N LEU A 106
SHEET 3 AA3 3 ARG A 155 TYR A 159 -1 N VAL A 158 O HIS A 166
SHEET 1 AA4 4 TYR E 54 GLN E 58 0
SHEET 2 AA4 4 ARG E 43 THR E 48 -1 N PHE E 45 O GLN E 58
SHEET 3 AA4 4 LYS E 77 TYR E 84 -1 O ASP E 79 N SER E 46
SHEET 4 AA4 4 ALA E 101 GLU E 103 -1 O GLU E 103 N VAL E 83
SHEET 1 AA5 4 TYR E 54 GLN E 58 0
SHEET 2 AA5 4 ARG E 43 THR E 48 -1 N PHE E 45 O GLN E 58
SHEET 3 AA5 4 LYS E 77 TYR E 84 -1 O ASP E 79 N SER E 46
SHEET 4 AA5 4 LEU E 317 LYS E 318 -1 O LEU E 317 N ILE E 80
SHEET 1 AA6 3 LEU E 106 ASP E 111 0
SHEET 2 AA6 3 GLY E 164 VAL E 169 -1 O VAL E 169 N LEU E 106
SHEET 3 AA6 3 ARG E 155 TYR E 159 -1 N VAL E 158 O HIS E 166
LINK OD1 ASP A 109 MN MN A 502 1555 1555 2.22
LINK OD2 ASP A 109 MN MN A 503 1555 1555 2.20
LINK OD1 ASP A 111 MN MN A 502 1555 1555 2.10
LINK OD2 ASP A 111 MN MN A 503 1555 1555 2.17
LINK SG CYS A 121 ZN ZN A 501 1555 1555 2.20
LINK SG CYS A 122 ZN ZN A 501 1555 1555 2.29
LINK SG CYS A 128 ZN ZN A 501 1555 1555 2.25
LINK SG CYS A 131 ZN ZN A 501 1555 1555 2.40
LINK OD2 ASP A 306 MN MN A 503 1555 1555 2.18
LINK MN MN A 502 O2A HFD A 504 1555 1555 2.09
LINK MN MN A 502 O2B HFD A 504 1555 1555 2.17
LINK MN MN A 502 O2G HFD A 504 1555 1555 2.05
LINK MN MN A 502 O HOH A 635 1555 1555 2.18
LINK MN MN A 503 O2A HFD A 504 1555 1555 2.52
LINK MN MN A 503 O HOH A 662 1555 1555 2.55
LINK OD1 ASP E 109 MN MN E 502 1555 1555 2.25
LINK OD2 ASP E 109 MN MN E 503 1555 1555 2.16
LINK OD1 ASP E 111 MN MN E 502 1555 1555 2.10
LINK OD2 ASP E 111 MN MN E 503 1555 1555 2.22
LINK SG CYS E 121 ZN ZN E 501 1555 1555 2.22
LINK SG CYS E 122 ZN ZN E 501 1555 1555 2.21
LINK SG CYS E 128 ZN ZN E 501 1555 1555 2.32
LINK SG CYS E 131 ZN ZN E 501 1555 1555 2.39
LINK OD2 ASP E 306 MN MN E 503 1555 1555 2.12
LINK MN MN E 502 O2A HFD E 504 1555 1555 2.21
LINK MN MN E 502 O2B HFD E 504 1555 1555 1.93
LINK MN MN E 502 O2G HFD E 504 1555 1555 2.33
LINK MN MN E 502 O HOH E 629 1555 1555 2.12
LINK MN MN E 503 O2A HFD E 504 1555 1555 2.51
LINK MN MN E 503 O HOH E 638 1555 1555 2.53
SITE 1 AC1 4 CYS A 121 CYS A 122 CYS A 128 CYS A 131
SITE 1 AC2 5 ASP A 109 ASP A 111 MN A 503 HFD A 504
SITE 2 AC2 5 HOH A 635
SITE 1 AC3 6 ASP A 109 ASP A 111 ASP A 306 MN A 502
SITE 2 AC3 6 HFD A 504 HOH A 662
SITE 1 AC4 19 LYS A 77 ASP A 79 ASP A 109 ASP A 111
SITE 2 AC4 19 SER A 160 ARG A 162 ARG A 163 HIS A 166
SITE 3 AC4 19 HIS A 315 LEU A 316 LEU A 317 LYS A 318
SITE 4 AC4 19 HIS A 324 MN A 502 MN A 503 HOH A 626
SITE 5 AC4 19 HOH A 635 HOH A 661 HOH A 664
SITE 1 AC5 4 CYS E 121 CYS E 122 CYS E 128 CYS E 131
SITE 1 AC6 5 ASP E 109 ASP E 111 MN E 503 HFD E 504
SITE 2 AC6 5 HOH E 629
SITE 1 AC7 6 ASP E 109 ASP E 111 ASP E 306 MN E 502
SITE 2 AC7 6 HFD E 504 HOH E 638
SITE 1 AC8 19 TYR E 54 ARG E 56 LYS E 77 ASP E 79
SITE 2 AC8 19 ASP E 109 ASP E 111 SER E 160 ARG E 162
SITE 3 AC8 19 ARG E 163 HIS E 166 HIS E 315 LEU E 316
SITE 4 AC8 19 LEU E 317 LYS E 318 HIS E 324 MN E 502
SITE 5 AC8 19 MN E 503 HOH E 615 HOH E 629
SITE 1 AC9 5 LEU E 204 SER E 205 GLU E 206 ASN E 281
SITE 2 AC9 5 TRP E 291
CRYST1 110.830 117.570 148.800 90.00 90.00 90.00 C 2 2 21 16
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 0.009023 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008506 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006720 0.00000