10 20 30 40 50 60 70 80 1KDN - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PHOSPHOTRANSFERASE 10-SEP-96 1KDN
TITLE STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_TAXID: 44689; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS TRANSFERASE, KINASE, ATP-BINDING, PHOSPHOTRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.CHERFILS,Y.W.XU,S.MORERA,J.JANIN
REVDAT 3 13-JUL-11 1KDN 1 VERSN REVDAT 2 24-FEB-09 1KDN 1 VERSN REVDAT 1 21-APR-97 1KDN 0
JRNL AUTH Y.W.XU,S.MORERA,J.JANIN,J.CHERFILS JRNL TITL ALF3 MIMICS THE TRANSITION STATE OF PROTEIN PHOSPHORYLATION JRNL TITL 2 IN THE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE JRNL TITL 3 AND MGADP. JRNL REF PROC.NATL.ACAD.SCI.USA V. 94 3579 1997 JRNL REFN ISSN 0027-8424 JRNL PMID 9108019 JRNL DOI 10.1073/PNAS.94.8.3579
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MORERA,M.CHIADMI,G.LEBRAS,I.LASCU,J.JANIN REMARK 1 TITL MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE REMARK 1 TITL 2 KINASE: X-RAY STRUCTURES OF THE PHOSPHOHISTIDINE REMARK 1 TITL 3 INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND REMARK 1 TITL 4 DICTYOSTELIUM REMARK 1 REF BIOCHEMISTRY V. 34 11062 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.MORERA,I.LASCU,C.DUMAS,G.LEBRAS,P.BRIOZZO,M.VERON,J.JANIN REMARK 1 TITL ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF REMARK 1 TITL 2 NUCLEOSIDE DIPHOSPHATE KINASE REMARK 1 REF BIOCHEMISTRY V. 33 459 1994 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL 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 : 29606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 3441 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 332 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.00 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) : 0.17 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.17 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.86 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 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 1KDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.906 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30088 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.16467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 102.32933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 102.32933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.16467 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 20390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 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 -0.500000 -0.866025 0.000000 107.03100 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 61.79438 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.16467
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 SER A 2 REMARK 465 THR A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 5 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 ASN B 4 REMARK 465 LYS B 5 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 THR C 3 REMARK 465 ASN C 4 REMARK 465 LYS C 5
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 C 155 CG GLU C 155 CD -0.095 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 LEU C 136 CA - CB - CG ANGL. DEV. = 15.0 DEGREES 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 ILE A 120 -44.48 68.92 REMARK 500 ASN B 7 17.64 -68.17 REMARK 500 VAL B 114 -15.42 -141.07 REMARK 500 ILE B 120 -44.70 61.48 REMARK 500 TYR C 56 33.26 -94.75 REMARK 500 ILE C 120 -44.83 63.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 120 25.0 L L OUTSIDE RANGE 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 920 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH B 863 DISTANCE = 5.11 ANGSTROMS REMARK 525 HOH B 869 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH C 909 DISTANCE = 5.08 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 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AF3 A 157 F3 REMARK 620 2 ADP A 158 O1B 89.8 REMARK 620 3 ADP A 158 O1A 94.5 85.5 REMARK 620 4 HOH A 671 O 80.0 167.6 88.3 REMARK 620 5 HOH A 698 O 174.6 94.7 82.8 95.2 REMARK 620 6 HOH A 690 O 94.4 86.9 168.2 100.8 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AF3 B 157 F3 REMARK 620 2 ADP B 158 O1A 94.0 REMARK 620 3 HOH B 847 O 162.7 78.6 REMARK 620 4 HOH B 604 O 84.2 86.5 110.5 REMARK 620 5 ADP B 158 O1B 82.8 71.9 80.1 153.9 REMARK 620 6 HOH B 669 O 90.4 160.5 91.8 112.9 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AF3 C 157 F3 REMARK 620 2 ADP C 158 O1B 86.1 REMARK 620 3 ADP C 158 O1A 94.4 81.1 REMARK 620 4 HOH C 667 O 90.7 89.8 169.1 REMARK 620 5 HOH C 766 O 167.3 85.7 74.7 98.9 REMARK 620 6 HOH C 722 O 84.7 165.6 88.7 101.3 101.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AF3 C 157 AL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP C 158 O3B REMARK 620 2 AF3 C 157 F1 77.6 REMARK 620 3 AF3 C 157 F2 97.4 125.4 REMARK 620 4 AF3 C 157 F3 90.3 118.5 115.9 REMARK 620 5 ADP C 158 O1B 45.4 70.5 139.1 59.7 REMARK 620 6 HIS C 122 ND1 166.9 93.5 95.6 85.7 122.8 REMARK 620 7 MG C 156 MG 76.7 98.0 134.3 22.2 38.7 95.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AF3 A 157 AL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 158 O1B REMARK 620 2 AF3 A 157 F1 136.4 REMARK 620 3 AF3 A 157 F2 67.7 121.9 REMARK 620 4 AF3 A 157 F3 57.9 129.1 108.6 REMARK 620 5 ADP A 158 O3B 46.7 90.2 83.5 89.8 REMARK 620 6 MG A 156 MG 37.3 142.8 91.0 21.2 75.6 REMARK 620 7 HIS A 122 ND1 116.4 107.2 79.6 86.3 160.4 94.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AF3 B 157 AL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP B 158 O3B REMARK 620 2 AF3 B 157 F1 90.9 REMARK 620 3 AF3 B 157 F2 86.2 126.4 REMARK 620 4 AF3 B 157 F3 93.5 116.6 117.0 REMARK 620 5 MG B 156 MG 80.8 132.3 100.0 20.5 REMARK 620 6 ADP B 158 O1B 47.8 135.3 74.6 60.7 41.2 REMARK 620 7 HIS B 122 ND1 174.0 94.9 89.0 85.5 96.5 127.2 REMARK 620 N 1 2 3 4 5 6
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 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 A 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 B 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 C 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP C 158
DBREF 1KDN A 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 1KDN B 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 1KDN C 1 155 UNP P22887 NDKC_DICDI 1 155
SEQRES 1 A 155 MET SER THR ASN LYS VAL ASN LYS GLU ARG THR PHE LEU SEQRES 2 A 155 ALA VAL LYS PRO ASP GLY VAL ALA ARG GLY LEU VAL GLY SEQRES 3 A 155 GLU ILE ILE ALA ARG TYR GLU LYS LYS GLY PHE VAL LEU SEQRES 4 A 155 VAL GLY LEU LYS GLN LEU VAL PRO THR LYS ASP LEU ALA SEQRES 5 A 155 GLU SER HIS TYR ALA GLU HIS LYS GLU ARG PRO PHE PHE SEQRES 6 A 155 GLY GLY LEU VAL SER PHE ILE THR SER GLY PRO VAL VAL SEQRES 7 A 155 ALA MET VAL PHE GLU GLY LYS GLY VAL VAL ALA SER ALA SEQRES 8 A 155 ARG LEU MET ILE GLY VAL THR ASN PRO LEU ALA SER ALA SEQRES 9 A 155 PRO GLY SER ILE ARG GLY ASP PHE GLY VAL ASP VAL GLY SEQRES 10 A 155 ARG ASN ILE ILE HIS GLY SER ASP SER VAL GLU SER ALA SEQRES 11 A 155 ASN ARG GLU ILE ALA LEU TRP PHE LYS PRO GLU GLU LEU SEQRES 12 A 155 LEU THR GLU VAL LYS PRO ASN PRO ASN LEU TYR GLU SEQRES 1 B 155 MET SER THR ASN LYS VAL ASN LYS GLU ARG THR PHE LEU SEQRES 2 B 155 ALA VAL LYS PRO ASP GLY VAL ALA ARG GLY LEU VAL GLY SEQRES 3 B 155 GLU ILE ILE ALA ARG TYR GLU LYS LYS GLY PHE VAL LEU SEQRES 4 B 155 VAL GLY LEU LYS GLN LEU VAL PRO THR LYS ASP LEU ALA SEQRES 5 B 155 GLU SER HIS TYR ALA GLU HIS LYS GLU ARG PRO PHE PHE SEQRES 6 B 155 GLY GLY LEU VAL SER PHE ILE THR SER GLY PRO VAL VAL SEQRES 7 B 155 ALA MET VAL PHE GLU GLY LYS GLY VAL VAL ALA SER ALA SEQRES 8 B 155 ARG LEU MET ILE GLY VAL THR ASN PRO LEU ALA SER ALA SEQRES 9 B 155 PRO GLY SER ILE ARG GLY ASP PHE GLY VAL ASP VAL GLY SEQRES 10 B 155 ARG ASN ILE ILE HIS GLY SER ASP SER VAL GLU SER ALA SEQRES 11 B 155 ASN ARG GLU ILE ALA LEU TRP PHE LYS PRO GLU GLU LEU SEQRES 12 B 155 LEU THR GLU VAL LYS PRO ASN PRO ASN LEU TYR GLU SEQRES 1 C 155 MET SER THR ASN LYS VAL ASN LYS GLU ARG THR PHE LEU SEQRES 2 C 155 ALA VAL LYS PRO ASP GLY VAL ALA ARG GLY LEU VAL GLY SEQRES 3 C 155 GLU ILE ILE ALA ARG TYR GLU LYS LYS GLY PHE VAL LEU SEQRES 4 C 155 VAL GLY LEU LYS GLN LEU VAL PRO THR LYS ASP LEU ALA SEQRES 5 C 155 GLU SER HIS TYR ALA GLU HIS LYS GLU ARG PRO PHE PHE SEQRES 6 C 155 GLY GLY LEU VAL SER PHE ILE THR SER GLY PRO VAL VAL SEQRES 7 C 155 ALA MET VAL PHE GLU GLY LYS GLY VAL VAL ALA SER ALA SEQRES 8 C 155 ARG LEU MET ILE GLY VAL THR ASN PRO LEU ALA SER ALA SEQRES 9 C 155 PRO GLY SER ILE ARG GLY ASP PHE GLY VAL ASP VAL GLY SEQRES 10 C 155 ARG ASN ILE ILE HIS GLY SER ASP SER VAL GLU SER ALA SEQRES 11 C 155 ASN ARG GLU ILE ALA LEU TRP PHE LYS PRO GLU GLU LEU SEQRES 12 C 155 LEU THR GLU VAL LYS PRO ASN PRO ASN LEU TYR GLU
HET MG A 156 1 HET MG B 156 1 HET MG C 156 1 HET AF3 A 157 4 HET ADP A 158 27 HET AF3 B 157 4 HET ADP B 158 27 HET AF3 C 157 4 HET ADP C 158 27
HETNAM MG MAGNESIUM ION HETNAM AF3 ALUMINUM FLUORIDE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
FORMUL 4 MG 3(MG 2+) FORMUL 7 AF3 3(AL F3) FORMUL 8 ADP 3(C10 H15 N5 O10 P2) FORMUL 13 HOH *332(H2 O)
HELIX 1 1 PRO A 17 ALA A 21 1 5 HELIX 2 2 VAL A 25 LYS A 35 1 11 HELIX 3 3 LYS A 49 HIS A 55 1 7 HELIX 4 4 ALA A 57 HIS A 59 5 3 HELIX 5 5 PHE A 65 ILE A 72 1 8 HELIX 6 6 VAL A 87 ILE A 95 1 9 HELIX 7 7 PRO A 100 ALA A 102 5 3 HELIX 8 8 ILE A 108 PHE A 112 1 5 HELIX 9 9 VAL A 116 ARG A 118 5 3 HELIX 10 10 VAL A 127 TRP A 137 1 11 HELIX 11 11 PRO A 140 GLU A 142 5 3 HELIX 12 12 PRO B 17 ALA B 21 1 5 HELIX 13 13 VAL B 25 LYS B 35 1 11 HELIX 14 14 LYS B 49 HIS B 55 1 7 HELIX 15 15 ALA B 57 HIS B 59 5 3 HELIX 16 16 PHE B 65 ILE B 72 1 8 HELIX 17 17 VAL B 87 ILE B 95 1 9 HELIX 18 18 PRO B 100 ALA B 102 5 3 HELIX 19 19 ILE B 108 PHE B 112 1 5 HELIX 20 20 VAL B 127 TRP B 137 1 11 HELIX 21 21 PRO B 140 GLU B 142 5 3 HELIX 22 22 PRO C 17 ALA C 21 1 5 HELIX 23 23 VAL C 25 LYS C 35 1 11 HELIX 24 24 LYS C 49 HIS C 55 1 7 HELIX 25 25 ALA C 57 HIS C 59 5 3 HELIX 26 26 PHE C 65 ILE C 72 1 8 HELIX 27 27 VAL C 87 ILE C 95 1 9 HELIX 28 28 PRO C 100 ALA C 102 5 3 HELIX 29 29 ILE C 108 PHE C 112 1 5 HELIX 30 30 VAL C 127 TRP C 137 1 11 HELIX 31 31 PRO C 140 GLU C 142 5 3
SHEET 1 A 4 ILE A 121 GLY A 123 0 SHEET 2 A 4 ARG A 10 VAL A 15 -1 N ALA A 14 O HIS A 122 SHEET 3 A 4 PRO A 76 GLU A 83 -1 N PHE A 82 O THR A 11 SHEET 4 A 4 VAL A 38 VAL A 46 -1 N LEU A 45 O VAL A 77 SHEET 1 B 4 ILE B 121 GLY B 123 0 SHEET 2 B 4 ARG B 10 VAL B 15 -1 N ALA B 14 O HIS B 122 SHEET 3 B 4 PRO B 76 GLU B 83 -1 N PHE B 82 O THR B 11 SHEET 4 B 4 VAL B 38 VAL B 46 -1 N LEU B 45 O VAL B 77 SHEET 1 C 4 ILE C 121 GLY C 123 0 SHEET 2 C 4 ARG C 10 VAL C 15 -1 N ALA C 14 O HIS C 122 SHEET 3 C 4 PRO C 76 GLU C 83 -1 N PHE C 82 O THR C 11 SHEET 4 C 4 VAL C 38 VAL C 46 -1 N LEU C 45 O VAL C 77
LINK MG MG A 156 F3 AF3 A 157 1555 1555 1.86 LINK MG MG A 156 O1B ADP A 158 1555 1555 2.23 LINK MG MG A 156 O1A ADP A 158 1555 1555 2.14 LINK MG MG B 156 F3 AF3 B 157 1555 1555 1.90 LINK MG MG B 156 O1A ADP B 158 1555 1555 2.38 LINK MG MG C 156 F3 AF3 C 157 1555 1555 2.03 LINK MG MG C 156 O1B ADP C 158 1555 1555 2.36 LINK MG MG C 156 O1A ADP C 158 1555 1555 2.11 LINK AL AF3 C 157 O3B ADP C 158 1555 1555 2.39 LINK MG MG A 156 O HOH A 671 1555 1555 2.19 LINK MG MG A 156 O HOH A 698 1555 1555 2.18 LINK MG MG A 156 O HOH A 690 1555 1555 2.01 LINK AL AF3 A 157 O1B ADP A 158 1555 1555 3.42 LINK AL AF3 A 157 O3B ADP A 158 1555 1555 2.41 LINK AL AF3 A 157 MG MG A 156 1555 1555 3.54 LINK AL AF3 A 157 ND1 HIS A 122 1555 1555 2.43 LINK MG MG B 156 O HOH B 847 1555 1555 1.80 LINK MG MG B 156 O HOH B 604 1555 1555 2.15 LINK MG MG B 156 O1B ADP B 158 1555 1555 2.41 LINK MG MG B 156 O HOH B 669 1555 1555 2.18 LINK AL AF3 B 157 O3B ADP B 158 1555 1555 2.45 LINK AL AF3 B 157 MG MG B 156 1555 1555 3.54 LINK AL AF3 B 157 O1B ADP B 158 1555 1555 3.29 LINK AL AF3 B 157 ND1 HIS B 122 1555 1555 2.58 LINK MG MG C 156 O HOH C 667 1555 1555 2.19 LINK MG MG C 156 O HOH C 766 1555 1555 2.00 LINK MG MG C 156 O HOH C 722 1555 1555 2.16 LINK AL AF3 C 157 O1B ADP C 158 1555 1555 3.48 LINK AL AF3 C 157 ND1 HIS C 122 1555 1555 2.48 LINK AL AF3 C 157 MG MG C 156 1555 1555 3.63
SITE 1 AC1 5 AF3 A 157 ADP A 158 HOH A 671 HOH A 690 SITE 2 AC1 5 HOH A 698 SITE 1 AC2 5 AF3 B 157 ADP B 158 HOH B 604 HOH B 669 SITE 2 AC2 5 HOH B 847 SITE 1 AC3 5 AF3 C 157 ADP C 158 HOH C 667 HOH C 722 SITE 2 AC3 5 HOH C 766 SITE 1 AC4 10 LYS A 16 TYR A 56 ARG A 92 ARG A 109 SITE 2 AC4 10 HIS A 122 GLY A 123 MG A 156 ADP A 158 SITE 3 AC4 10 HOH A 671 HOH A 690 SITE 1 AC5 16 LYS A 16 HIS A 59 PHE A 64 LEU A 68 SITE 2 AC5 16 ARG A 92 THR A 98 ARG A 109 VAL A 116 SITE 3 AC5 16 ASN A 119 MG A 156 AF3 A 157 HOH A 671 SITE 4 AC5 16 HOH A 690 HOH A 698 HOH A 728 HOH A 793 SITE 1 AC6 10 LYS B 16 TYR B 56 ARG B 92 ARG B 109 SITE 2 AC6 10 HIS B 122 GLY B 123 MG B 156 ADP B 158 SITE 3 AC6 10 HOH B 604 HOH B 669 SITE 1 AC7 17 HOH A 676 LYS B 16 TYR B 56 HIS B 59 SITE 2 AC7 17 PHE B 64 LEU B 68 ARG B 92 THR B 98 SITE 3 AC7 17 ARG B 109 VAL B 116 ASN B 119 MG B 156 SITE 4 AC7 17 AF3 B 157 HOH B 776 HOH B 792 HOH B 826 SITE 5 AC7 17 HOH B 847 SITE 1 AC8 10 LYS C 16 TYR C 56 ARG C 92 ARG C 109 SITE 2 AC8 10 HIS C 122 GLY C 123 MG C 156 ADP C 158 SITE 3 AC8 10 HOH C 667 HOH C 722 SITE 1 AC9 14 LYS C 16 HIS C 59 PHE C 64 LEU C 68 SITE 2 AC9 14 ARG C 92 THR C 98 ARG C 109 VAL C 116 SITE 3 AC9 14 ASN C 119 MG C 156 AF3 C 157 HOH C 722 SITE 4 AC9 14 HOH C 766 HOH C 845
CRYST1 71.354 71.354 153.494 90.00 90.00 120.00 P 31 2 1 18
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 0.014015 0.008091 0.000000 0.00000
SCALE2 0.000000 0.016183 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006515 0.00000