HEADER REPLICATION 24-MAR-19 6R4S TITLE CRYSTAL STRUCTURE OF THE PRI1 SUBUNIT OF HUMAN PRIMASE BOUND TO ATP 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 6R4S 1 LINK REVDAT 2 02-OCT-19 6R4S 1 JRNL REVDAT 1 11-SEP-19 6R4S 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. 2.75 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 25616 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 6R4S 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_1292100912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-15 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 : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97898 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25616 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 29.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 4.950 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : 1.040 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 (%): 50.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 75.61500 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 75.61500 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 55.06500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.06500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.61500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.06500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.63500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.61500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.06500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.63500 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 ILE A 360 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 ARG A 381 REMARK 465 LYS A 407 REMARK 465 GLY E -2 REMARK 465 THR E -1 REMARK 465 SER E 0 REMARK 465 MET E 1 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 465 LYS E 407 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 SER A 160 HZ1 LYS A 318 1.47 REMARK 500 HH TYR A 32 OE2 GLU A 105 1.56 REMARK 500 HH11 ARG E 329 O VAL E 347 1.56 REMARK 500 OD1 ASP A 116 HH21 ARG A 119 1.59 REMARK 500 OD1 ASP A 143 HE1 TRP A 157 1.60 REMARK 500 OD1 ASN E 62 OG SER E 64 2.14 REMARK 500 O LEU E 234 NE ARG E 268 2.17 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 LEU A 49 -167.74 -100.33 REMARK 500 SER A 124 -134.47 59.98 REMARK 500 ARG A 162 -72.20 -145.41 REMARK 500 VAL A 229 -57.60 -126.13 REMARK 500 SER E 124 -136.46 61.82 REMARK 500 ARG E 162 -72.94 -146.86 REMARK 500 VAL E 229 -55.01 -123.59 REMARK 500 SER E 331 93.69 -69.92 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 93.1 REMARK 620 3 ATP A 504 O2G 178.6 88.2 REMARK 620 4 ATP A 504 O2B 95.7 167.6 83.1 REMARK 620 5 ATP A 504 O2A 105.2 87.4 75.3 81.8 REMARK 620 6 HOH A 608 O 86.1 91.5 93.3 97.8 168.6 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 101.0 REMARK 620 3 ASP A 306 OD2 109.5 103.2 REMARK 620 N 1 2 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 112.9 REMARK 620 3 CYS A 128 SG 94.2 99.5 REMARK 620 4 CYS A 131 SG 120.5 117.2 106.8 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 90.5 REMARK 620 3 ATP E 504 O2G 169.5 81.2 REMARK 620 4 ATP E 504 O2A 115.4 91.1 71.5 REMARK 620 5 ATP E 504 O2B 105.2 164.3 83.3 81.4 REMARK 620 6 HOH E 604 O 74.0 80.6 98.1 167.8 104.3 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 94.7 REMARK 620 3 ASP E 306 OD2 93.1 104.7 REMARK 620 4 ATP E 504 O2A 81.8 83.6 170.6 REMARK 620 N 1 2 3 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 116.0 REMARK 620 3 CYS E 128 SG 91.5 94.8 REMARK 620 4 CYS E 131 SG 109.2 127.7 109.1 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 ATP 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 ATP E 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6R5D 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 6R4S A 1 407 UNP P49642 PRI1_HUMAN 1 407 DBREF 6R4S E 1 407 UNP P49642 PRI1_HUMAN 1 407 SEQADV 6R4S GLY A -2 UNP P49642 EXPRESSION TAG SEQADV 6R4S THR A -1 UNP P49642 EXPRESSION TAG SEQADV 6R4S SER A 0 UNP P49642 EXPRESSION TAG SEQADV 6R4S GLY E -2 UNP P49642 EXPRESSION TAG SEQADV 6R4S THR E -1 UNP P49642 EXPRESSION TAG SEQADV 6R4S 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 ATP A 504 43 HET ZN E 501 1 HET MN E 502 1 HET MN E 503 1 HET ATP E 504 43 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MN 4(MN 2+) FORMUL 6 ATP 2(C10 H16 N5 O13 P3) FORMUL 11 HOH *44(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 ASP A 171 LYS A 176 1 6 HELIX 10 AB1 SER A 178 LEU A 189 1 12 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 SER A 405 1 18 HELIX 23 AC5 GLU E 8 LEU E 20 1 13 HELIX 24 AC6 PRO E 22 TYR E 32 1 11 HELIX 25 AC7 GLY E 33 VAL E 35 5 3 HELIX 26 AC8 LYS E 50 ASP E 52 5 3 HELIX 27 AC9 ASN E 62 ASN E 74 1 13 HELIX 28 AD1 ARG E 87 HIS E 91 5 5 HELIX 29 AD2 THR E 113 ASP E 116 5 4 HELIX 30 AD3 TRP E 132 ASP E 149 1 18 HELIX 31 AD4 ASP E 171 LYS E 176 1 6 HELIX 32 AD5 SER E 178 LEU E 189 1 12 HELIX 33 AD6 HIS E 209 LEU E 228 1 20 HELIX 34 AD7 ASN E 236 ALA E 245 1 10 HELIX 35 AD8 LEU E 246 VAL E 247 5 2 HELIX 36 AD9 PRO E 248 THR E 250 5 3 HELIX 37 AE1 ILE E 251 SER E 262 1 12 HELIX 38 AE2 ASN E 264 ARG E 278 1 15 HELIX 39 AE3 PRO E 290 PHE E 302 1 13 HELIX 40 AE4 ILE E 307 GLY E 312 1 6 HELIX 41 AE5 ASP E 335 PHE E 342 5 8 HELIX 42 AE6 THR E 349 ALA E 359 1 11 HELIX 43 AE7 ASP E 382 THR E 386 5 5 HELIX 44 AE8 LEU E 388 SER E 405 1 18 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 47 O ILE A 55 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 47 O ILE A 55 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 165 N ILE A 110 SHEET 3 AA3 3 ARG A 155 TYR A 159 -1 N LEU A 156 O TRP A 168 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 47 O ILE E 55 SHEET 3 AA4 4 LYS E 77 TYR E 84 -1 O GLY E 81 N GLU E 44 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 47 O ILE E 55 SHEET 3 AA5 4 LYS E 77 TYR E 84 -1 O GLY E 81 N GLU E 44 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 165 N ILE E 110 SHEET 3 AA6 3 ARG E 155 TYR E 159 -1 N LEU E 156 O TRP E 168 LINK OD1 ASP A 109 MN MN A 502 1555 1555 2.18 LINK OD2 ASP A 109 MN MN A 503 1555 1555 2.17 LINK OD1 ASP A 111 MN MN A 502 1555 1555 2.10 LINK OD2 ASP A 111 MN MN A 503 1555 1555 2.13 LINK SG CYS A 121 ZN ZN A 501 1555 1555 2.22 LINK SG CYS A 122 ZN ZN A 501 1555 1555 2.42 LINK SG CYS A 128 ZN ZN A 501 1555 1555 2.34 LINK SG CYS A 131 ZN ZN A 501 1555 1555 2.39 LINK OD2 ASP A 306 MN MN A 503 1555 1555 2.22 LINK MN MN A 502 O2G ATP A 504 1555 1555 2.00 LINK MN MN A 502 O2B ATP A 504 1555 1555 2.03 LINK MN MN A 502 O2A ATP A 504 1555 1555 2.29 LINK MN MN A 502 O HOH A 608 1555 1555 2.23 LINK OD1 ASP E 109 MN MN E 502 1555 1555 2.18 LINK OD2 ASP E 109 MN MN E 503 1555 1555 2.15 LINK OD1 ASP E 111 MN MN E 502 1555 1555 2.14 LINK OD2 ASP E 111 MN MN E 503 1555 1555 2.16 LINK SG CYS E 121 ZN ZN E 501 1555 1555 2.28 LINK SG CYS E 122 ZN ZN E 501 1555 1555 2.26 LINK SG CYS E 128 ZN ZN E 501 1555 1555 2.30 LINK SG CYS E 131 ZN ZN E 501 1555 1555 2.59 LINK OD2 ASP E 306 MN MN E 503 1555 1555 2.13 LINK MN MN E 502 O2G ATP E 504 1555 1555 2.09 LINK MN MN E 502 O2A ATP E 504 1555 1555 2.30 LINK MN MN E 502 O2B ATP E 504 1555 1555 1.97 LINK MN MN E 502 O HOH E 604 1555 1555 2.24 LINK MN MN E 503 O2A ATP E 504 1555 1555 2.61 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 HIS A 166 ATP A 504 SITE 2 AC2 5 HOH A 608 SITE 1 AC3 4 ASP A 109 ASP A 111 ASP A 306 ATP A 504 SITE 1 AC4 15 ASP A 79 ASP A 109 ASP A 111 SER A 160 SITE 2 AC4 15 ARG A 162 ARG A 163 HIS A 166 LEU A 316 SITE 3 AC4 15 LEU A 317 LYS A 318 HIS A 324 MN A 502 SITE 4 AC4 15 MN A 503 HOH A 608 HOH A 610 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 HIS E 166 ATP E 504 SITE 2 AC6 5 HOH E 604 SITE 1 AC7 4 ASP E 109 ASP E 111 ASP E 306 ATP E 504 SITE 1 AC8 15 TYR E 54 LYS E 77 ASP E 79 ASP E 109 SITE 2 AC8 15 ASP E 111 SER E 160 ARG E 162 ARG E 163 SITE 3 AC8 15 HIS E 166 LEU E 316 LEU E 317 LYS E 318 SITE 4 AC8 15 HIS E 324 MN E 502 MN E 503 CRYST1 110.130 117.270 151.230 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 0.009080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006612 0.00000