HEADER REPLICATION 24-MAR-19 6R5D TITLE CRYSTAL STRUCTURE OF THE PRI1 SUBUNIT OF HUMAN PRIMASE BOUND TO DATP 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 6R5D 1 LINK REVDAT 2 02-OCT-19 6R5D 1 JRNL REVDAT 1 11-SEP-19 6R5D 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. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260.0000 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 71364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3571 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 6R5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292100922. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-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 : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91741 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 : 71418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 46.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.750 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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 FOR SHELL : 1.330 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 (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 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 75.86000 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 75.86000 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 55.26000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.64500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.26000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.64500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.86000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.26000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.64500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.86000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.26000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.64500 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 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 GLY E -2 REMARK 465 THR E -1 REMARK 465 SER E 0 REMARK 465 MET E 1 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: 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 E 663 O HOH E 772 2.00 REMARK 500 O HOH E 688 O HOH E 720 2.14 REMARK 500 O HOH A 745 O HOH A 765 2.19 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 TYR A 32 59.26 39.10 REMARK 500 LEU A 49 -158.33 -101.41 REMARK 500 ASN A 62 -173.68 -171.26 REMARK 500 ASN A 74 67.84 38.27 REMARK 500 SER A 124 -132.68 62.23 REMARK 500 ARG A 162 -56.16 -142.80 REMARK 500 ARG A 163 21.65 -141.00 REMARK 500 LEU A 191 -30.34 -134.81 REMARK 500 VAL A 229 -62.90 -103.94 REMARK 500 PHE E 4 147.16 -172.76 REMARK 500 LEU E 49 -162.02 -103.06 REMARK 500 ASN E 62 -179.64 -173.37 REMARK 500 SER E 124 -133.60 59.52 REMARK 500 ARG E 162 -71.65 -141.13 REMARK 500 VAL E 229 -64.63 -103.81 REMARK 500 THR E 250 -4.80 -59.95 REMARK 500 ASP E 306 84.54 -62.75 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 96.6 REMARK 620 3 DTP A 504 O2G 166.7 84.7 REMARK 620 4 DTP A 504 O2B 91.8 171.3 86.6 REMARK 620 5 DTP A 504 O2A 108.3 95.7 84.6 83.9 REMARK 620 6 HOH A 650 O 78.4 86.1 88.5 93.3 172.8 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 97.3 REMARK 620 3 ASP A 306 OD2 91.7 94.6 REMARK 620 4 DTP A 504 O2A 85.2 94.2 171.0 REMARK 620 5 HOH A 696 O 94.4 164.3 74.7 97.2 REMARK 620 6 HOH A 762 O 158.4 104.1 89.2 90.6 65.1 REMARK 620 N 1 2 3 4 5 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 122.1 REMARK 620 3 CYS A 128 SG 105.5 101.8 REMARK 620 4 CYS A 131 SG 103.9 108.3 116.0 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 88.1 REMARK 620 3 DTP E 504 O2B 101.0 170.9 REMARK 620 4 DTP E 504 O2A 105.5 94.5 82.7 REMARK 620 5 DTP E 504 O2G 169.4 85.8 85.3 83.6 REMARK 620 6 HOH E 699 O 79.3 84.8 97.2 175.1 91.5 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 111.5 REMARK 620 3 ASP E 306 OD2 98.7 97.0 REMARK 620 4 DTP E 504 O2A 81.1 93.1 169.2 REMARK 620 5 HOH E 675 O 100.5 147.7 82.1 87.3 REMARK 620 6 HOH E 688 O 153.3 89.7 94.5 81.6 58.4 REMARK 620 N 1 2 3 4 5 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 119.2 REMARK 620 3 CYS E 128 SG 102.5 99.1 REMARK 620 4 CYS E 131 SG 107.3 112.2 116.4 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 DTP A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN E 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN E 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTP E 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO E 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6R4S RELATED DB: PDB REMARK 900 RELATED ID: 6R5E RELATED DB: PDB REMARK 900 RELATED ID: 6R4T RELATED DB: PDB REMARK 900 RELATED ID: 6R4U RELATED DB: PDB REMARK 900 RELATED ID: 6RB4 RELATED DB: PDB DBREF 6R5D A 1 407 UNP P49642 PRI1_HUMAN 1 407 DBREF 6R5D E 1 407 UNP P49642 PRI1_HUMAN 1 407 SEQADV 6R5D GLY A -2 UNP P49642 EXPRESSION TAG SEQADV 6R5D THR A -1 UNP P49642 EXPRESSION TAG SEQADV 6R5D SER A 0 UNP P49642 EXPRESSION TAG SEQADV 6R5D GLY E -2 UNP P49642 EXPRESSION TAG SEQADV 6R5D THR E -1 UNP P49642 EXPRESSION TAG SEQADV 6R5D 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 DTP A 504 42 HET EDO A 505 10 HET EDO A 506 10 HET EDO A 507 10 HET EDO A 508 10 HET EDO A 509 10 HET EDO A 510 10 HET EDO A 511 10 HET ZN E 501 1 HET MN E 502 1 HET MN E 503 1 HET DTP E 504 42 HET EDO E 505 10 HET EDO E 506 10 HET EDO E 507 10 HET EDO E 508 10 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MN 4(MN 2+) FORMUL 6 DTP 2(C10 H16 N5 O12 P3) FORMUL 7 EDO 11(C2 H6 O2) FORMUL 22 HOH *376(H2 O) HELIX 1 AA1 GLU A 8 LEU A 20 1 13 HELIX 2 AA2 PRO A 22 ASN A 31 1 10 HELIX 3 AA3 TYR A 32 VAL A 35 5 4 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 VAL A 94 5 8 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 178 SER A 190 1 13 HELIX 10 AB1 HIS A 209 LEU A 228 1 20 HELIX 11 AB2 ASN A 236 ALA A 245 1 10 HELIX 12 AB3 LEU A 246 VAL A 247 5 2 HELIX 13 AB4 PRO A 248 THR A 250 5 3 HELIX 14 AB5 ILE A 251 SER A 262 1 12 HELIX 15 AB6 ASN A 264 SER A 277 1 14 HELIX 16 AB7 PRO A 290 PHE A 302 1 13 HELIX 17 AB8 ASP A 306 GLY A 312 1 7 HELIX 18 AB9 ASP A 335 PHE A 342 5 8 HELIX 19 AC1 ASP A 343 VAL A 347 5 5 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 ASN E 31 1 10 HELIX 26 AC8 TYR E 32 VAL E 35 5 4 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 VAL E 94 5 8 HELIX 30 AD3 THR E 113 ASP E 116 5 4 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 TYR E 279 1 16 HELIX 40 AE4 PRO E 290 PHE E 302 1 13 HELIX 41 AE5 ILE E 307 GLY E 312 1 6 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 ILE E 360 5 3 HELIX 46 AF1 ASP E 382 THR E 386 5 5 HELIX 47 AF2 LEU E 388 ARG E 406 1 19 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 GLY A 81 N GLU A 44 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 GLY A 81 N GLU A 44 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 2.23 LINK OD2 ASP A 109 MN MN A 503 1555 1555 2.14 LINK OD1 ASP A 111 MN MN A 502 1555 1555 2.13 LINK OD2 ASP A 111 MN MN A 503 1555 1555 2.19 LINK SG CYS A 121 ZN ZN A 501 1555 1555 2.26 LINK SG CYS A 122 ZN ZN A 501 1555 1555 2.34 LINK SG CYS A 128 ZN ZN A 501 1555 1555 2.40 LINK SG CYS A 131 ZN ZN A 501 1555 1555 2.40 LINK OD2 ASP A 306 MN MN A 503 1555 1555 2.17 LINK MN MN A 502 O2G DTP A 504 1555 1555 2.40 LINK MN MN A 502 O2B DTP A 504 1555 1555 2.18 LINK MN MN A 502 O2A DTP A 504 1555 1555 2.11 LINK MN MN A 502 O HOH A 650 1555 1555 1.99 LINK MN MN A 503 O2A DTP A 504 1555 1555 2.49 LINK MN MN A 503 O HOH A 696 1555 1555 2.56 LINK MN MN A 503 O HOH A 762 1555 1555 2.51 LINK OD1 ASP E 109 MN MN E 502 1555 1555 2.25 LINK OD2 ASP E 109 MN MN E 503 1555 1555 2.17 LINK OD1 ASP E 111 MN MN E 502 1555 1555 2.15 LINK OD2 ASP E 111 MN MN E 503 1555 1555 2.19 LINK SG CYS E 121 ZN ZN E 501 1555 1555 2.33 LINK SG CYS E 122 ZN ZN E 501 1555 1555 2.30 LINK SG CYS E 128 ZN ZN E 501 1555 1555 2.38 LINK SG CYS E 131 ZN ZN E 501 1555 1555 2.40 LINK OD2 ASP E 306 MN MN E 503 1555 1555 2.18 LINK MN MN E 502 O2B DTP E 504 1555 1555 2.03 LINK MN MN E 502 O2A DTP E 504 1555 1555 2.25 LINK MN MN E 502 O2G DTP E 504 1555 1555 2.44 LINK MN MN E 502 O HOH E 699 1555 1555 2.25 LINK MN MN E 503 O2A DTP E 504 1555 1555 2.35 LINK MN MN E 503 O HOH E 675 1555 1555 2.50 LINK MN MN E 503 O HOH E 688 1555 1555 2.38 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 DTP A 504 SITE 2 AC2 5 HOH A 650 SITE 1 AC3 7 ASP A 109 ASP A 111 ASP A 306 MN A 502 SITE 2 AC3 7 DTP A 504 HOH A 696 HOH A 762 SITE 1 AC4 16 ASP A 109 ASP A 111 SER A 160 ARG A 162 SITE 2 AC4 16 ARG A 163 HIS A 166 HIS A 315 LEU A 316 SITE 3 AC4 16 LEU A 317 LYS A 318 HIS A 324 MN A 502 SITE 4 AC4 16 MN A 503 HOH A 623 HOH A 650 HOH A 696 SITE 1 AC5 6 THR A 349 SER A 351 ASP E 149 PHE E 150 SITE 2 AC5 6 TYR E 188 HOH E 648 SITE 1 AC6 5 ASP A 126 ILE A 127 EDO A 510 HOH A 642 SITE 2 AC6 5 SER E 173 SITE 1 AC7 5 LYS A 153 HIS A 154 ARG A 155 ASN A 401 SITE 2 AC7 5 HOH A 660 SITE 1 AC8 3 HOH A 630 HOH A 637 ARG E 355 SITE 1 AC9 4 ASN A 217 LYS A 220 TRP A 294 ASP E 51 SITE 1 AD1 4 TYR A 159 ARG A 329 PRO A 344 EDO A 506 SITE 1 AD2 2 ARG A 19 ARG A 381 SITE 1 AD3 4 CYS E 121 CYS E 122 CYS E 128 CYS E 131 SITE 1 AD4 5 ASP E 109 ASP E 111 MN E 503 DTP E 504 SITE 2 AD4 5 HOH E 699 SITE 1 AD5 7 ASP E 109 ASP E 111 ASP E 306 MN E 502 SITE 2 AD5 7 DTP E 504 HOH E 675 HOH E 688 SITE 1 AD6 19 ARG A 278 TYR E 54 ASP E 79 ASP E 109 SITE 2 AD6 19 ASP E 111 SER E 160 ARG E 162 ARG E 163 SITE 3 AD6 19 HIS E 166 HIS E 315 LEU E 316 LEU E 317 SITE 4 AD6 19 LYS E 318 HIS E 324 MN E 502 MN E 503 SITE 5 AD6 19 HOH E 663 HOH E 675 HOH E 688 SITE 1 AD7 3 SER A 173 ASP E 343 PHE E 345 SITE 1 AD8 5 ASP A 149 PHE A 150 TYR A 188 THR E 349 SITE 2 AD8 5 SER E 351 SITE 1 AD9 6 ILE A 360 LEU E 191 LYS E 201 VAL E 202 SITE 2 AD9 6 HIS E 203 HOH E 707 SITE 1 AE1 4 PHE E 342 ASP E 343 THR E 346 TYR E 391 CRYST1 110.520 117.290 151.720 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 0.009048 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006591 0.00000