HEADER TRANSFERASE 09-JUL-20 6XPU TITLE NUCLEOSIDE DIPHOSPHATE KINASE FROM ASPERGILLUS FUMGIATUS AF293 BOUND TITLE 2 TO IDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NDP KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS FUMIGATUS AF293; SOURCE 3 ORGANISM_TAXID: 330879; SOURCE 4 STRAIN: ATCC MYA-4609 / AF293 / CBS 101355 / FGSC A1100; SOURCE 5 GENE: NDK1, AFUA_5G03490; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NUCLEOSIDE DIPHOSPHATE KINASE, PHOSPHOTRANSFERASE, KINASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NGUYEN,J.B.BRUNING REVDAT 3 18-OCT-23 6XPU 1 REMARK REVDAT 2 14-APR-21 6XPU 1 JRNL REVDAT 1 04-NOV-20 6XPU 0 JRNL AUTH S.NGUYEN,B.JOVCEVSKI,T.L.PUKALA,J.B.BRUNING JRNL TITL NUCLEOSIDE SELECTIVITY OF ASPERGILLUS FUMIGATUS JRNL TITL 2 NUCLEOSIDE-DIPHOSPHATE KINASE. JRNL REF FEBS J. V. 288 2398 2021 JRNL REFN ISSN 1742-464X JRNL PMID 33089641 JRNL DOI 10.1111/FEBS.15607 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35668 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 : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1797 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 42.2700 - 4.4659 1.00 2809 142 0.1528 0.1821 REMARK 3 2 4.4659 - 3.5453 1.00 2648 145 0.1306 0.1661 REMARK 3 3 3.5453 - 3.0973 1.00 2639 148 0.1537 0.2066 REMARK 3 4 3.0973 - 2.8142 1.00 2610 140 0.1855 0.2533 REMARK 3 5 2.8142 - 2.6125 1.00 2613 132 0.1967 0.2537 REMARK 3 6 2.6125 - 2.4585 1.00 2569 148 0.2083 0.2850 REMARK 3 7 2.4585 - 2.3354 1.00 2565 160 0.2064 0.2581 REMARK 3 8 2.3354 - 2.2337 0.99 2591 122 0.2127 0.2696 REMARK 3 9 2.2337 - 2.1477 0.99 2543 130 0.2128 0.2934 REMARK 3 10 2.1477 - 2.0736 1.00 2615 122 0.2035 0.2420 REMARK 3 11 2.0736 - 2.0088 1.00 2549 144 0.2073 0.2689 REMARK 3 12 2.0088 - 1.9514 1.00 2560 129 0.2131 0.2674 REMARK 3 13 1.9514 - 1.9000 1.00 2560 135 0.2513 0.3210 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.67 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 6XPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000247267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-18 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20161205 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35832 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.271 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 0.57500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 2.8.2 REMARK 200 STARTING MODEL: 6XP7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19.5% PEG 3350, 0.20 M NACL, 0.1 M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.56650 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.56650 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -178.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 -1.000000 0.000000 0.000000 52.90000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 383 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 542 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 578 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 459 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 486 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 153 REMARK 465 MET B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 GLY B -1 REMARK 465 ALA B 153 REMARK 465 MET C -8 REMARK 465 HIS C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 GLY C -1 REMARK 465 ALA C 153 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 LEU A 96 CG CD1 CD2 REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 LYS C 84 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 121 N CA C O CB OG 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 ILE A 109 -50.96 -133.47 REMARK 500 ILE A 109 -52.28 -133.47 REMARK 500 VAL A 115 -15.49 60.29 REMARK 500 VAL A 115 -47.09 70.46 REMARK 500 SER B 41 79.06 -112.07 REMARK 500 ILE B 109 -49.42 -130.20 REMARK 500 ILE B 109 -48.28 -130.20 REMARK 500 VAL B 115 -41.34 71.88 REMARK 500 VAL B 115 -10.52 59.42 REMARK 500 ILE C 109 -51.10 -131.79 REMARK 500 ILE C 109 -50.26 -131.79 REMARK 500 VAL C 115 -40.62 71.43 REMARK 500 VAL C 115 -10.68 57.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 595 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 596 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 597 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 598 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A 599 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH A 600 DISTANCE = 7.86 ANGSTROMS REMARK 525 HOH A 601 DISTANCE = 8.50 ANGSTROMS REMARK 525 HOH B 571 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH B 572 DISTANCE = 7.05 ANGSTROMS REMARK 525 HOH B 573 DISTANCE = 7.57 ANGSTROMS REMARK 525 HOH B 574 DISTANCE = 7.99 ANGSTROMS REMARK 525 HOH B 575 DISTANCE = 8.07 ANGSTROMS REMARK 525 HOH B 576 DISTANCE = 8.08 ANGSTROMS REMARK 525 HOH B 577 DISTANCE = 9.12 ANGSTROMS REMARK 525 HOH B 578 DISTANCE = 10.56 ANGSTROMS REMARK 525 HOH C 540 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH C 541 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH C 542 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH C 543 DISTANCE = 8.25 ANGSTROMS 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IDP A 202 O2A REMARK 620 2 HOH A 315 O 91.6 REMARK 620 3 HOH A 319 O 71.9 82.2 REMARK 620 4 HOH A 466 O 86.7 169.1 87.1 REMARK 620 5 HOH A 475 O 168.6 86.2 96.7 93.3 REMARK 620 6 HOH A 521 O 114.6 101.6 172.1 88.8 76.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IDP B 202 O2A REMARK 620 2 HOH B 310 O 90.0 REMARK 620 3 HOH B 328 O 82.4 169.9 REMARK 620 4 HOH B 375 O 82.5 85.3 87.1 REMARK 620 5 HOH B 407 O 101.0 98.8 89.2 174.5 REMARK 620 6 HOH B 449 O 172.3 93.7 93.1 91.0 85.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IDP C 202 O1A REMARK 620 2 HOH C 324 O 85.2 REMARK 620 3 HOH C 347 O 83.2 86.3 REMARK 620 4 HOH C 351 O 89.9 173.3 97.5 REMARK 620 5 HOH C 405 O 99.1 83.8 169.7 92.6 REMARK 620 6 HOH C 465 O 176.7 97.9 96.0 87.1 82.3 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 MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IDP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IDP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IDP C 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XP4 RELATED DB: PDB REMARK 900 6XP4 CONTAINS THE SAME PROTEIN IN AN UNBOUND STATE REMARK 900 RELATED ID: 6XP7 RELATED DB: PDB REMARK 900 6XP7 CONTAINS THE SAME PROTEIN BOUND TO ADP DBREF 6XPU A 1 153 UNP Q7Z8P9 NDK_ASPFU 1 153 DBREF 6XPU B 1 153 UNP Q7Z8P9 NDK_ASPFU 1 153 DBREF 6XPU C 1 153 UNP Q7Z8P9 NDK_ASPFU 1 153 SEQADV 6XPU MET A -8 UNP Q7Z8P9 INITIATING METHIONINE SEQADV 6XPU HIS A -7 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS A -6 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS A -5 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS A -4 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS A -3 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS A -2 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU GLY A -1 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU SER A 0 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU MET B -8 UNP Q7Z8P9 INITIATING METHIONINE SEQADV 6XPU HIS B -7 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS B -6 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS B -5 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS B -4 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS B -3 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS B -2 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU GLY B -1 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU SER B 0 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU MET C -8 UNP Q7Z8P9 INITIATING METHIONINE SEQADV 6XPU HIS C -7 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS C -6 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS C -5 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS C -4 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS C -3 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU HIS C -2 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU GLY C -1 UNP Q7Z8P9 EXPRESSION TAG SEQADV 6XPU SER C 0 UNP Q7Z8P9 EXPRESSION TAG SEQRES 1 A 162 MET HIS HIS HIS HIS HIS HIS GLY SER MET SER ASN GLU SEQRES 2 A 162 GLN THR PHE ILE ALA ILE LYS PRO ASP GLY VAL GLN ARG SEQRES 3 A 162 GLY LEU ILE GLY PRO ILE ILE SER ARG PHE GLU ASN ARG SEQRES 4 A 162 GLY PHE LYS LEU VAL ALA MET LYS LEU VAL SER PRO PRO SEQRES 5 A 162 GLN SER GLN LEU GLU GLN HIS TYR ALA ASP LEU SER ASP SEQRES 6 A 162 LYS PRO PHE PHE LYS GLY LEU VAL SER TYR MET LEU SER SEQRES 7 A 162 GLY PRO ILE CYS ALA MET VAL TRP GLU GLY ARG ASP VAL SEQRES 8 A 162 VAL LYS THR GLY ARG THR ILE LEU GLY ALA THR ASN PRO SEQRES 9 A 162 LEU ALA SER ALA PRO GLY THR ILE ARG GLY ASP PHE ALA SEQRES 10 A 162 ILE ASP VAL GLY ARG ASN VAL CYS HIS GLY SER ASP SER SEQRES 11 A 162 VAL GLU ASN ALA LYS LYS GLU ILE ALA LEU TRP PHE LYS SEQRES 12 A 162 PRO GLU GLU LEU ILE SER TRP LYS SER ALA THR PHE ASP SEQRES 13 A 162 TRP VAL TYR GLU LYS ALA SEQRES 1 B 162 MET HIS HIS HIS HIS HIS HIS GLY SER MET SER ASN GLU SEQRES 2 B 162 GLN THR PHE ILE ALA ILE LYS PRO ASP GLY VAL GLN ARG SEQRES 3 B 162 GLY LEU ILE GLY PRO ILE ILE SER ARG PHE GLU ASN ARG SEQRES 4 B 162 GLY PHE LYS LEU VAL ALA MET LYS LEU VAL SER PRO PRO SEQRES 5 B 162 GLN SER GLN LEU GLU GLN HIS TYR ALA ASP LEU SER ASP SEQRES 6 B 162 LYS PRO PHE PHE LYS GLY LEU VAL SER TYR MET LEU SER SEQRES 7 B 162 GLY PRO ILE CYS ALA MET VAL TRP GLU GLY ARG ASP VAL SEQRES 8 B 162 VAL LYS THR GLY ARG THR ILE LEU GLY ALA THR ASN PRO SEQRES 9 B 162 LEU ALA SER ALA PRO GLY THR ILE ARG GLY ASP PHE ALA SEQRES 10 B 162 ILE ASP VAL GLY ARG ASN VAL CYS HIS GLY SER ASP SER SEQRES 11 B 162 VAL GLU ASN ALA LYS LYS GLU ILE ALA LEU TRP PHE LYS SEQRES 12 B 162 PRO GLU GLU LEU ILE SER TRP LYS SER ALA THR PHE ASP SEQRES 13 B 162 TRP VAL TYR GLU LYS ALA SEQRES 1 C 162 MET HIS HIS HIS HIS HIS HIS GLY SER MET SER ASN GLU SEQRES 2 C 162 GLN THR PHE ILE ALA ILE LYS PRO ASP GLY VAL GLN ARG SEQRES 3 C 162 GLY LEU ILE GLY PRO ILE ILE SER ARG PHE GLU ASN ARG SEQRES 4 C 162 GLY PHE LYS LEU VAL ALA MET LYS LEU VAL SER PRO PRO SEQRES 5 C 162 GLN SER GLN LEU GLU GLN HIS TYR ALA ASP LEU SER ASP SEQRES 6 C 162 LYS PRO PHE PHE LYS GLY LEU VAL SER TYR MET LEU SER SEQRES 7 C 162 GLY PRO ILE CYS ALA MET VAL TRP GLU GLY ARG ASP VAL SEQRES 8 C 162 VAL LYS THR GLY ARG THR ILE LEU GLY ALA THR ASN PRO SEQRES 9 C 162 LEU ALA SER ALA PRO GLY THR ILE ARG GLY ASP PHE ALA SEQRES 10 C 162 ILE ASP VAL GLY ARG ASN VAL CYS HIS GLY SER ASP SER SEQRES 11 C 162 VAL GLU ASN ALA LYS LYS GLU ILE ALA LEU TRP PHE LYS SEQRES 12 C 162 PRO GLU GLU LEU ILE SER TRP LYS SER ALA THR PHE ASP SEQRES 13 C 162 TRP VAL TYR GLU LYS ALA HET MG A 201 1 HET IDP A 202 27 HET MG B 201 1 HET IDP B 202 27 HET MG C 201 1 HET IDP C 202 27 HETNAM MG MAGNESIUM ION HETNAM IDP INOSINE-5'-DIPHOSPHATE FORMUL 4 MG 3(MG 2+) FORMUL 5 IDP 3(C10 H14 N4 O11 P2) FORMUL 10 HOH *822(H2 O) HELIX 1 AA1 LYS A 11 ARG A 17 1 7 HELIX 2 AA2 LEU A 19 GLY A 31 1 13 HELIX 3 AA3 PRO A 43 TYR A 51 1 9 HELIX 4 AA4 ALA A 52 SER A 55 5 4 HELIX 5 AA5 PHE A 59 LEU A 68 1 10 HELIX 6 AA6 ASP A 81 GLY A 91 1 11 HELIX 7 AA7 ASN A 94 SER A 98 5 5 HELIX 8 AA8 THR A 102 ALA A 108 1 7 HELIX 9 AA9 ASP A 110 ASN A 114 5 5 HELIX 10 AB1 SER A 121 PHE A 133 1 13 HELIX 11 AB2 LYS A 134 LEU A 138 5 5 HELIX 12 AB3 THR A 145 TYR A 150 1 6 HELIX 13 AB4 LYS B 11 ARG B 17 1 7 HELIX 14 AB5 LEU B 19 GLY B 31 1 13 HELIX 15 AB6 PRO B 43 TYR B 51 1 9 HELIX 16 AB7 ALA B 52 SER B 55 5 4 HELIX 17 AB8 PHE B 59 LEU B 68 1 10 HELIX 18 AB9 ASP B 81 GLY B 91 1 11 HELIX 19 AC1 ASN B 94 SER B 98 5 5 HELIX 20 AC2 THR B 102 ALA B 108 1 7 HELIX 21 AC3 ASP B 110 ASN B 114 5 5 HELIX 22 AC4 SER B 121 PHE B 133 1 13 HELIX 23 AC5 LYS B 134 LEU B 138 5 5 HELIX 24 AC6 THR B 145 TYR B 150 1 6 HELIX 25 AC7 LYS C 11 ARG C 17 1 7 HELIX 26 AC8 LEU C 19 GLY C 31 1 13 HELIX 27 AC9 PRO C 43 TYR C 51 1 9 HELIX 28 AD1 ALA C 52 SER C 55 5 4 HELIX 29 AD2 PHE C 59 SER C 69 1 11 HELIX 30 AD3 ASP C 81 GLY C 91 1 11 HELIX 31 AD4 ASN C 94 SER C 98 5 5 HELIX 32 AD5 THR C 102 ALA C 108 1 7 HELIX 33 AD6 ASP C 110 ASN C 114 5 5 HELIX 34 AD7 SER C 121 PHE C 133 1 13 HELIX 35 AD8 LYS C 134 LEU C 138 5 5 HELIX 36 AD9 THR C 145 TYR C 150 1 6 SHEET 1 AA1 4 LYS A 33 VAL A 40 0 SHEET 2 AA1 4 ILE A 72 GLU A 78 -1 O ILE A 72 N VAL A 40 SHEET 3 AA1 4 GLN A 5 ILE A 10 -1 N ILE A 10 O CYS A 73 SHEET 4 AA1 4 CYS A 116 GLY A 118 -1 O HIS A 117 N ALA A 9 SHEET 1 AA2 4 LYS B 33 VAL B 40 0 SHEET 2 AA2 4 ILE B 72 GLU B 78 -1 O GLU B 78 N LYS B 33 SHEET 3 AA2 4 GLN B 5 ILE B 10 -1 N THR B 6 O TRP B 77 SHEET 4 AA2 4 CYS B 116 GLY B 118 -1 O HIS B 117 N ALA B 9 SHEET 1 AA3 4 LYS C 33 VAL C 40 0 SHEET 2 AA3 4 ILE C 72 GLU C 78 -1 O GLU C 78 N LYS C 33 SHEET 3 AA3 4 GLN C 5 ILE C 10 -1 N ILE C 10 O CYS C 73 SHEET 4 AA3 4 CYS C 116 GLY C 118 -1 O HIS C 117 N ALA C 9 LINK MG MG A 201 O2A IDP A 202 1555 1555 2.20 LINK MG MG A 201 O HOH A 315 1555 1555 2.07 LINK MG MG A 201 O HOH A 319 1555 1555 2.13 LINK MG MG A 201 O HOH A 466 1555 1555 2.35 LINK MG MG A 201 O HOH A 475 1555 1555 2.51 LINK MG MG A 201 O HOH A 521 1555 1555 2.20 LINK MG MG B 201 O2A IDP B 202 1555 1555 2.05 LINK MG MG B 201 O HOH B 310 1555 1555 2.14 LINK MG MG B 201 O HOH B 328 1555 1555 2.19 LINK MG MG B 201 O HOH B 375 1555 1555 2.16 LINK MG MG B 201 O HOH B 407 1555 1555 2.20 LINK MG MG B 201 O HOH B 449 1555 1555 2.13 LINK MG MG C 201 O1A IDP C 202 1555 1555 2.10 LINK MG MG C 201 O HOH C 324 1555 1555 2.30 LINK MG MG C 201 O HOH C 347 1555 1555 2.08 LINK MG MG C 201 O HOH C 351 1555 1555 2.14 LINK MG MG C 201 O HOH C 405 1555 1555 2.08 LINK MG MG C 201 O HOH C 465 1555 1555 2.50 SITE 1 AC1 6 IDP A 202 HOH A 315 HOH A 319 HOH A 466 SITE 2 AC1 6 HOH A 475 HOH A 521 SITE 1 AC2 23 LYS A 11 TYR A 51 LEU A 54 PHE A 59 SITE 2 AC2 23 LEU A 63 ARG A 87 THR A 93 VAL A 111 SITE 3 AC2 23 GLY A 112 ASN A 114 MG A 201 HOH A 303 SITE 4 AC2 23 HOH A 306 HOH A 310 HOH A 315 HOH A 319 SITE 5 AC2 23 HOH A 321 HOH A 328 HOH A 335 HOH A 371 SITE 6 AC2 23 HOH A 438 HOH A 444 GLU C 151 SITE 1 AC3 7 ASP B 53 IDP B 202 HOH B 310 HOH B 328 SITE 2 AC3 7 HOH B 375 HOH B 407 HOH B 449 SITE 1 AC4 20 GLU A 151 LYS B 11 TYR B 51 LEU B 54 SITE 2 AC4 20 PHE B 59 LEU B 63 ARG B 87 THR B 93 SITE 3 AC4 20 VAL B 111 ASN B 114 MG B 201 HOH B 310 SITE 4 AC4 20 HOH B 312 HOH B 315 HOH B 320 HOH B 325 SITE 5 AC4 20 HOH B 328 HOH B 375 HOH B 391 HOH B 442 SITE 1 AC5 6 IDP C 202 HOH C 324 HOH C 347 HOH C 351 SITE 2 AC5 6 HOH C 405 HOH C 465 SITE 1 AC6 20 GLU B 151 LYS C 11 TYR C 51 LEU C 54 SITE 2 AC6 20 PHE C 59 LEU C 63 ARG C 87 THR C 93 SITE 3 AC6 20 VAL C 111 ASN C 114 MG C 201 HOH C 302 SITE 4 AC6 20 HOH C 313 HOH C 318 HOH C 324 HOH C 347 SITE 5 AC6 20 HOH C 351 HOH C 361 HOH C 392 HOH C 417 CRYST1 52.900 70.307 119.133 90.00 90.00 90.00 P 21 2 21 12 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 0.018904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008394 0.00000