PDB Short entry for 1UCN HEADER TRANSFERASE 16-APR-03 1UCN TITLE X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED TITLE 2 WITH ADP AT 2 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE A; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PJC20 KEYWDS MUTANT COMPLEXE ADP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,S.GALLOIS-MONTBRUN,B.SCHNEIDER,M.VERON,S.MORERA,D.DEVILLE- AUTHOR 2 BONNE,J.JANIN REVDAT 4 10-NOV-21 1UCN 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1UCN 1 VERSN REVDAT 2 24-FEB-09 1UCN 1 VERSN REVDAT 1 30-SEP-03 1UCN 0 JRNL AUTH Y.CHEN,S.GALLOIS-MONTBRUN,B.SCHNEIDER,M.VERON,S.MORERA, JRNL AUTH 2 D.DEVILLE-BONNE,J.JANIN JRNL TITL NUCLEOTIDE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASES: X-RAY JRNL TITL 2 STRUCTURE OF HUMAN NDPK-A IN COMPLEX WITH ADP AND COMPARISON JRNL TITL 3 TO PROTEIN KINASES JRNL REF J.MOL.BIOL. V. 332 915 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12972261 JRNL DOI 10.1016/J.JMB.2003.07.004 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 42480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2132 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 2132 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3585 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 109 REMARK 3 SOLVENT ATOMS : 336 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UCN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005680. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, ATP, TRIS-HCL, MGCL, DTT, REMARK 280 HEPES, CALCIUM ACETATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 45.64600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 58.03750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 58.03750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.82300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 58.03750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 58.03750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 68.46900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 58.03750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.03750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.82300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 58.03750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.03750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 68.46900 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.64600 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: X,Y,Z * REMARK 300 -X,-Y,1/2+Z * REMARK 300 1/2-Y,1/2+X,1/4+Z * REMARK 300 1/2+Y,1/2-X,3/4+Z * REMARK 300 1/2-X,1/2+Y,1/4-Z * REMARK 300 1/2+X,1/2-Y,3/4-Z * REMARK 300 Y,X,-Z * REMARK 300 -Y,-X,1/2-Z * 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 23670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -285.0 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 0.000000 -1.000000 0.000000 116.07500 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 116.07500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 45.64600 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 1 REMARK 465 MET B 1 REMARK 465 MET C 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 3220 O HOH C 3220 8665 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 50 CD GLU A 50 OE2 0.079 REMARK 500 GLU B 50 CD GLU B 50 OE2 0.078 REMARK 500 GLU C 50 CD GLU C 50 OE2 0.075 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 ASN A 3 125.34 57.16 REMARK 500 GLU A 93 158.82 -48.58 REMARK 500 ILE A 110 -51.17 -121.12 REMARK 500 ASN A 115 32.44 -96.09 REMARK 500 ILE A 116 -16.12 41.50 REMARK 500 PRO A 136 -28.37 -38.66 REMARK 500 ASN B 3 135.20 146.63 REMARK 500 ILE B 116 -13.98 39.12 REMARK 500 ASN C 3 134.87 150.42 REMARK 500 ASP C 54 -6.70 -55.19 REMARK 500 ASP C 57 44.85 -88.86 REMARK 500 PRO C 59 4.21 -56.08 REMARK 500 TRP C 60 17.93 -149.17 REMARK 500 ILE C 110 -52.55 -126.11 REMARK 500 ILE C 116 -22.02 38.07 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 CA A1162 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 119 O REMARK 620 2 ASP A 121 OD2 86.7 REMARK 620 3 ADP A1160 O1B 115.5 78.4 REMARK 620 4 ADP A1160 O1A 169.4 103.2 63.9 REMARK 620 5 HOH A1192 O 99.3 73.3 133.3 87.4 REMARK 620 6 HOH A1226 O 81.5 124.3 153.9 95.7 55.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2162 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 119 O REMARK 620 2 ADP B2160 O1B 94.7 REMARK 620 3 ADP B2160 O1A 157.4 65.2 REMARK 620 4 HOH B2236 O 97.8 145.9 94.4 REMARK 620 5 HOH B2261 O 78.0 68.1 84.6 83.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 131 O REMARK 620 2 HOH B2241 O 96.5 REMARK 620 3 HOH B2289 O 68.0 92.9 REMARK 620 4 HOH B2298 O 79.1 50.5 127.3 REMARK 620 5 HOH B2313 O 92.3 149.0 63.1 160.3 REMARK 620 6 HOH B2314 O 91.4 139.3 126.8 92.6 69.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY C 131 O REMARK 620 2 HOH C3204 O 99.1 REMARK 620 3 HOH C3205 O 87.8 166.8 REMARK 620 4 HOH C3206 O 61.3 134.3 58.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C3162 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP C3160 O1A REMARK 620 2 ADP C3160 O1B 73.4 REMARK 620 3 HOH C3222 O 70.1 141.2 REMARK 620 4 HOH C3223 O 88.8 75.4 116.1 REMARK 620 5 HOH C3224 O 88.9 142.7 49.4 71.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 2161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 3161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 3162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 2160 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP C 3160 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NUE RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED REMARK 900 WITH GDP AT 2 A RESOLUITION DBREF 1UCN A 1 152 UNP P15531 NDKA_HUMAN 1 152 DBREF 1UCN B 1 152 UNP P15531 NDKA_HUMAN 1 152 DBREF 1UCN C 1 152 UNP P15531 NDKA_HUMAN 1 152 SEQADV 1UCN TRP A 60 UNP P15531 PHE 60 ENGINEERED MUTATION SEQADV 1UCN GLY A 118 UNP P15531 HIS 118 ENGINEERED MUTATION SEQADV 1UCN TRP B 60 UNP P15531 PHE 60 ENGINEERED MUTATION SEQADV 1UCN GLY B 118 UNP P15531 HIS 118 ENGINEERED MUTATION SEQADV 1UCN TRP C 60 UNP P15531 PHE 60 ENGINEERED MUTATION SEQADV 1UCN GLY C 118 UNP P15531 HIS 118 ENGINEERED MUTATION SEQRES 1 A 152 MET ALA ASN CYS GLU ARG THR PHE ILE ALA ILE LYS PRO SEQRES 2 A 152 ASP GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS SEQRES 3 A 152 ARG PHE GLU GLN LYS GLY PHE ARG LEU VAL GLY LEU LYS SEQRES 4 A 152 PHE MET GLN ALA SER GLU ASP LEU LEU LYS GLU HIS TYR SEQRES 5 A 152 VAL ASP LEU LYS ASP ARG PRO TRP PHE ALA GLY LEU VAL SEQRES 6 A 152 LYS TYR MET HIS SER GLY PRO VAL VAL ALA MET VAL TRP SEQRES 7 A 152 GLU GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU SEQRES 8 A 152 GLY GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE SEQRES 9 A 152 ARG GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE SEQRES 10 A 152 GLY GLY SER ASP SER VAL GLU SER ALA GLU LYS GLU ILE SEQRES 11 A 152 GLY LEU TRP PHE HIS PRO GLU GLU LEU VAL ASP TYR THR SEQRES 12 A 152 SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 B 152 MET ALA ASN CYS GLU ARG THR PHE ILE ALA ILE LYS PRO SEQRES 2 B 152 ASP GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS SEQRES 3 B 152 ARG PHE GLU GLN LYS GLY PHE ARG LEU VAL GLY LEU LYS SEQRES 4 B 152 PHE MET GLN ALA SER GLU ASP LEU LEU LYS GLU HIS TYR SEQRES 5 B 152 VAL ASP LEU LYS ASP ARG PRO TRP PHE ALA GLY LEU VAL SEQRES 6 B 152 LYS TYR MET HIS SER GLY PRO VAL VAL ALA MET VAL TRP SEQRES 7 B 152 GLU GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU SEQRES 8 B 152 GLY GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE SEQRES 9 B 152 ARG GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE SEQRES 10 B 152 GLY GLY SER ASP SER VAL GLU SER ALA GLU LYS GLU ILE SEQRES 11 B 152 GLY LEU TRP PHE HIS PRO GLU GLU LEU VAL ASP TYR THR SEQRES 12 B 152 SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 C 152 MET ALA ASN CYS GLU ARG THR PHE ILE ALA ILE LYS PRO SEQRES 2 C 152 ASP GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE LYS SEQRES 3 C 152 ARG PHE GLU GLN LYS GLY PHE ARG LEU VAL GLY LEU LYS SEQRES 4 C 152 PHE MET GLN ALA SER GLU ASP LEU LEU LYS GLU HIS TYR SEQRES 5 C 152 VAL ASP LEU LYS ASP ARG PRO TRP PHE ALA GLY LEU VAL SEQRES 6 C 152 LYS TYR MET HIS SER GLY PRO VAL VAL ALA MET VAL TRP SEQRES 7 C 152 GLU GLY LEU ASN VAL VAL LYS THR GLY ARG VAL MET LEU SEQRES 8 C 152 GLY GLU THR ASN PRO ALA ASP SER LYS PRO GLY THR ILE SEQRES 9 C 152 ARG GLY ASP PHE CYS ILE GLN VAL GLY ARG ASN ILE ILE SEQRES 10 C 152 GLY GLY SER ASP SER VAL GLU SER ALA GLU LYS GLU ILE SEQRES 11 C 152 GLY LEU TRP PHE HIS PRO GLU GLU LEU VAL ASP TYR THR SEQRES 12 C 152 SER CYS ALA GLN ASN TRP ILE TYR GLU HET PO4 A1161 5 HET CA A1162 1 HET ADP A1160 27 HET PO4 B2161 5 HET CA B2162 1 HET CA B1002 1 HET ADP B2160 27 HET TRS B1003 8 HET PO4 C3161 5 HET CA C3162 1 HET CA C1001 1 HET ADP C3160 27 HETNAM PO4 PHOSPHATE ION HETNAM CA CALCIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 4 PO4 3(O4 P 3-) FORMUL 5 CA 5(CA 2+) FORMUL 6 ADP 3(C10 H15 N5 O10 P2) FORMUL 11 TRS C4 H12 N O3 1+ FORMUL 16 HOH *336(H2 O) HELIX 1 1 LYS A 12 ARG A 18 1 7 HELIX 2 2 LEU A 20 GLY A 32 1 13 HELIX 3 3 SER A 44 TYR A 52 1 9 HELIX 4 4 VAL A 53 LYS A 56 5 4 HELIX 5 5 TRP A 60 SER A 70 1 11 HELIX 6 6 ASN A 82 GLY A 92 1 11 HELIX 7 7 ASN A 95 SER A 99 5 5 HELIX 8 8 THR A 103 CYS A 109 1 7 HELIX 9 9 GLN A 111 ASN A 115 5 5 HELIX 10 10 SER A 122 PHE A 134 1 13 HELIX 11 11 HIS A 135 LEU A 139 5 5 HELIX 12 12 ALA A 146 TYR A 151 1 6 HELIX 13 13 LYS B 12 ARG B 18 1 7 HELIX 14 14 LEU B 20 GLY B 32 1 13 HELIX 15 15 SER B 44 TYR B 52 1 9 HELIX 16 16 VAL B 53 LYS B 56 5 4 HELIX 17 17 TRP B 60 SER B 70 1 11 HELIX 18 18 ASN B 82 GLY B 92 1 11 HELIX 19 19 ASN B 95 SER B 99 5 5 HELIX 20 20 THR B 103 CYS B 109 1 7 HELIX 21 21 GLN B 111 ASN B 115 5 5 HELIX 22 22 SER B 122 PHE B 134 1 13 HELIX 23 23 HIS B 135 LEU B 139 5 5 HELIX 24 24 ALA B 146 TYR B 151 1 6 HELIX 25 25 LYS C 12 ARG C 18 1 7 HELIX 26 26 LEU C 20 GLY C 32 1 13 HELIX 27 27 SER C 44 TYR C 52 1 9 HELIX 28 28 VAL C 53 LYS C 56 5 4 HELIX 29 29 TRP C 60 SER C 70 1 11 HELIX 30 30 ASN C 82 GLY C 92 1 11 HELIX 31 31 ASN C 95 SER C 99 5 5 HELIX 32 32 THR C 103 CYS C 109 1 7 HELIX 33 33 GLN C 111 ASN C 115 5 5 HELIX 34 34 SER C 122 PHE C 134 1 13 HELIX 35 35 HIS C 135 LEU C 139 5 5 HELIX 36 36 ALA C 146 TYR C 151 1 6 SHEET 1 A 4 ARG A 34 MET A 41 0 SHEET 2 A 4 VAL A 73 GLU A 79 -1 O ALA A 75 N LYS A 39 SHEET 3 A 4 ARG A 6 ILE A 11 -1 N ILE A 9 O MET A 76 SHEET 4 A 4 ILE A 117 GLY A 119 -1 O GLY A 118 N ALA A 10 SHEET 1 B 4 ARG B 34 MET B 41 0 SHEET 2 B 4 VAL B 73 GLU B 79 -1 O ALA B 75 N LYS B 39 SHEET 3 B 4 ARG B 6 ILE B 11 -1 N ILE B 11 O VAL B 74 SHEET 4 B 4 ILE B 117 GLY B 119 -1 O GLY B 118 N ALA B 10 SHEET 1 C 4 ARG C 34 MET C 41 0 SHEET 2 C 4 VAL C 73 GLU C 79 -1 O VAL C 73 N MET C 41 SHEET 3 C 4 ARG C 6 ILE C 11 -1 N ILE C 9 O MET C 76 SHEET 4 C 4 ILE C 117 GLY C 119 -1 O GLY C 118 N ALA C 10 SSBOND 1 CYS A 4 CYS A 4 1555 7465 2.61 LINK O GLY A 119 CA CA A1162 1555 1555 3.07 LINK OD2 ASP A 121 CA CA A1162 1555 1555 2.55 LINK O1B ADP A1160 CA CA A1162 1555 1555 2.73 LINK O1A ADP A1160 CA CA A1162 1555 1555 2.44 LINK CA CA A1162 O HOH A1192 1555 1555 2.95 LINK CA CA A1162 O HOH A1226 1555 1555 2.27 LINK O GLY B 119 CA CA B2162 1555 1555 2.95 LINK O GLY B 131 CA CA B1002 1555 1555 2.59 LINK CA CA B1002 O HOH B2241 1555 1555 2.43 LINK CA CA B1002 O HOH B2289 1555 1555 2.69 LINK CA CA B1002 O HOH B2298 1555 1555 3.37 LINK CA CA B1002 O HOH B2313 1555 1555 2.44 LINK CA CA B1002 O HOH B2314 1555 1555 2.14 LINK O1B ADP B2160 CA CA B2162 1555 1555 2.40 LINK O1A ADP B2160 CA CA B2162 1555 1555 2.54 LINK CA CA B2162 O HOH B2236 1555 1555 3.00 LINK CA CA B2162 O HOH B2261 1555 1555 2.63 LINK O GLY C 131 CA CA C1001 1555 1555 2.82 LINK CA CA C1001 O HOH C3204 1555 1555 2.28 LINK CA CA C1001 O HOH C3205 1555 1555 2.69 LINK CA CA C1001 O HOH C3206 1555 1555 2.19 LINK O1A ADP C3160 CA CA C3162 1555 1555 2.32 LINK O1B ADP C3160 CA CA C3162 1555 1555 2.43 LINK CA CA C3162 O HOH C3222 1555 1555 3.16 LINK CA CA C3162 O HOH C3223 1555 1555 2.89 LINK CA CA C3162 O HOH C3224 1555 1555 2.74 SITE 1 AC1 8 ALA A 10 LYS A 12 HIS A 51 TYR A 52 SITE 2 AC1 8 GLY A 118 GLY A 119 CA A1162 HOH A1226 SITE 1 AC2 6 GLY A 119 ASP A 121 ADP A1160 PO4 A1161 SITE 2 AC2 6 HOH A1192 HOH A1226 SITE 1 AC3 7 LYS B 12 HIS B 51 TYR B 52 GLY B 118 SITE 2 AC3 7 GLY B 119 HOH B2236 HOH B2261 SITE 1 AC4 4 GLY B 119 ADP B2160 HOH B2236 HOH B2261 SITE 1 AC5 5 HIS C 51 TYR C 52 GLY C 118 GLY C 119 SITE 2 AC5 5 HOH C3223 SITE 1 AC6 3 ADP C3160 HOH C3223 HOH C3224 SITE 1 AC7 4 GLY C 131 HOH C3204 HOH C3205 HOH C3206 SITE 1 AC8 6 GLY B 131 PHE B 134 HOH B2241 HOH B2289 SITE 2 AC8 6 HOH B2313 HOH B2314 SITE 1 AC9 12 LYS A 12 LEU A 55 TRP A 60 LEU A 64 SITE 2 AC9 12 ARG A 88 THR A 94 ARG A 105 VAL A 112 SITE 3 AC9 12 ASN A 115 ASP A 121 CA A1162 HOH A1190 SITE 1 BC1 11 LYS B 12 LEU B 55 TRP B 60 ARG B 88 SITE 2 BC1 11 THR B 94 ARG B 105 VAL B 112 ASN B 115 SITE 3 BC1 11 CA B2162 HOH B2211 HOH B2261 SITE 1 BC2 10 LYS C 12 TRP C 60 LEU C 64 ARG C 88 SITE 2 BC2 10 THR C 94 ARG C 105 VAL C 112 ASN C 115 SITE 3 BC2 10 CA C3162 HOH C3223 SITE 1 BC3 3 GLU B 152 HOH B2312 GLU C 152 CRYST1 116.075 116.075 91.292 90.00 90.00 90.00 P 41 21 2 24 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 0.008615 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010954 0.00000