HEADER TRANSFERASE 09-DEC-05 2C95 TITLE STRUCTURE OF ADENYLATE KINASE 1 IN COMPLEX WITH P1,P4-DI(ADENOSINE) TITLE 2 TETRAPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATP-AMP TRANSPHOSPHORYLASE, AK1, MYOKINASE; COMPND 5 EC: 2.7.4.3; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLIC-SGC KEYWDS TRANSFERASE, AP4A, NUCLEOTIDE KINASE, TRANSFERASE ATP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.BUNKOCZI,P.FILIPPAKOPOULOS,A.JANSSON,E.LONGMAN,F.VON DELFT, AUTHOR 2 A.EDWARDS,C.ARROWSMITH,M.SUNDSTROM,S.KNAPP REVDAT 6 13-DEC-23 2C95 1 REMARK REVDAT 5 04-APR-18 2C95 1 REMARK REVDAT 4 24-JAN-18 2C95 1 AUTHOR JRNL REVDAT 3 13-JUL-11 2C95 1 VERSN REVDAT 2 24-FEB-09 2C95 1 VERSN REVDAT 1 20-FEB-07 2C95 0 JRNL AUTH G.BUNKOCZI,P.FILIPPAKOPOULOS,A.JANSSON,E.LONGMAN, JRNL AUTH 2 F.VON DELFT,A.EDWARDS,C.ARROWSMITH,M.SUNDSTROM,J.WEIGELT, JRNL AUTH 3 S.KNAPP JRNL TITL STRUCTURE OF ADENYLATE KINASE 1 IN COMPLEX WITH P1, JRNL TITL 2 P4-DI(ADENOSINE)TETRAPHOSPHATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 35815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1891 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 821 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2983 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 380 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : UNVERIFIED REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.43000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.249 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3205 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2177 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4354 ; 1.593 ; 2.032 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5333 ; 0.995 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 403 ; 5.767 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;36.526 ;24.328 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 577 ;13.692 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;12.573 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3499 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 613 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 630 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2269 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1527 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1595 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 264 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.176 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 64 ; 0.325 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.132 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2009 ; 1.656 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3141 ; 2.184 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1365 ; 4.047 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1205 ; 5.478 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 194 5 REMARK 3 1 B 0 B 194 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1128 ; 0.32 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 1319 ; 0.53 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1128 ; 0.84 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 1319 ; 1.59 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 194 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4686 17.1866 10.4825 REMARK 3 T TENSOR REMARK 3 T11: -0.0931 T22: -0.1187 REMARK 3 T33: -0.0948 T12: -0.0115 REMARK 3 T13: 0.0021 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 1.0643 L22: 1.0176 REMARK 3 L33: 1.5352 L12: -0.0476 REMARK 3 L13: -0.0023 L23: -0.4114 REMARK 3 S TENSOR REMARK 3 S11: -0.0241 S12: -0.0630 S13: -0.0415 REMARK 3 S21: 0.0795 S22: 0.0230 S23: 0.0569 REMARK 3 S31: -0.0644 S32: -0.0686 S33: 0.0012 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 194 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3978 51.8382 10.3093 REMARK 3 T TENSOR REMARK 3 T11: -0.0848 T22: -0.1306 REMARK 3 T33: -0.0807 T12: -0.0028 REMARK 3 T13: 0.0092 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 1.2074 L22: 0.6880 REMARK 3 L33: 1.9302 L12: 0.1037 REMARK 3 L13: 0.1474 L23: -0.3829 REMARK 3 S TENSOR REMARK 3 S11: -0.0238 S12: -0.0681 S13: -0.0258 REMARK 3 S21: 0.0378 S22: 0.0146 S23: 0.0294 REMARK 3 S31: -0.0267 S32: -0.0163 S33: 0.0091 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2C95 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC HR MULTILAYER OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37771 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 32.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 41.3 REMARK 200 DATA REDUNDANCY IN SHELL : 0.93 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1Z83 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.4 M NAMALONATE 1 MM ZNSO4, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 31.26750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.27900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.99900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.27900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.26750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.99900 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ASN A 195 REMARK 465 SER B 0 REMARK 465 MET B 1 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 GLU A 2 CG CD OE1 OE2 REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 LYS A 7 CD CE NZ REMARK 470 LYS A 56 CD CE NZ REMARK 470 LYS A 63 NZ REMARK 470 GLN A 100 CD OE1 NE2 REMARK 470 LYS A 166 CE NZ REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 GLU B 3 CG CD OE1 OE2 REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 LEU B 5 CG CD1 CD2 REMARK 470 LYS B 6 NZ REMARK 470 LYS B 7 CD CE NZ REMARK 470 LYS B 56 NZ REMARK 470 LYS B 83 CE NZ REMARK 470 LYS B 88 CE NZ REMARK 470 GLU B 144 CG CD OE1 OE2 REMARK 470 LYS B 155 CE NZ REMARK 470 LYS B 166 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2011 O HOH A 2093 2.17 REMARK 500 OE1 GLN A 30 O HOH A 2027 2.18 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 B 5 1.68 -64.99 REMARK 500 THR B 135 -38.99 -135.92 REMARK 500 SER B 136 59.51 -158.92 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 A2017 DISTANCE = 6.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B4P A1195 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A1196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B4P B1196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI B1197 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z83 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN AK1A IN COMPLEX WITH AP5A REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE FOR THE PROTEIN BELOW IS FROM A SYNTHETIC REMARK 999 CONSTRUCT (GENBANK ID AAQ02450) AND ACCOUNTS FOR THE REMARK 999 SEQUENCE CONFLICTS BELOW. HOWEVER, UNIPROT ENTRY P00568 REMARK 999 REMAINS THE CLOSEST MATCH TO THIS SEQUENCE. DBREF 2C95 A 1 193 UNP P00568 KAD1_HUMAN 1 193 DBREF 2C95 B 1 193 UNP P00568 KAD1_HUMAN 1 193 SEQADV 2C95 SER A 0 UNP P00568 EXPRESSION TAG SEQADV 2C95 ASN A 9 UNP P00568 LYS 9 CONFLICT SEQADV 2C95 LEU A 194 UNP P00568 CONFLICT SEQADV 2C95 ASN A 195 UNP P00568 EXPRESSION TAG SEQADV 2C95 SER B 0 UNP P00568 EXPRESSION TAG SEQADV 2C95 ASN B 9 UNP P00568 LYS 9 CONFLICT SEQADV 2C95 LEU B 194 UNP P00568 CONFLICT SEQADV 2C95 ASN B 195 UNP P00568 EXPRESSION TAG SEQRES 1 A 196 SER MET GLU GLU LYS LEU LYS LYS THR ASN ILE ILE PHE SEQRES 2 A 196 VAL VAL GLY GLY PRO GLY SER GLY LYS GLY THR GLN CYS SEQRES 3 A 196 GLU LYS ILE VAL GLN LYS TYR GLY TYR THR HIS LEU SER SEQRES 4 A 196 THR GLY ASP LEU LEU ARG SER GLU VAL SER SER GLY SER SEQRES 5 A 196 ALA ARG GLY LYS LYS LEU SER GLU ILE MET GLU LYS GLY SEQRES 6 A 196 GLN LEU VAL PRO LEU GLU THR VAL LEU ASP MET LEU ARG SEQRES 7 A 196 ASP ALA MET VAL ALA LYS VAL ASN THR SER LYS GLY PHE SEQRES 8 A 196 LEU ILE ASP GLY TYR PRO ARG GLU VAL GLN GLN GLY GLU SEQRES 9 A 196 GLU PHE GLU ARG ARG ILE GLY GLN PRO THR LEU LEU LEU SEQRES 10 A 196 TYR VAL ASP ALA GLY PRO GLU THR MET THR GLN ARG LEU SEQRES 11 A 196 LEU LYS ARG GLY GLU THR SER GLY ARG VAL ASP ASP ASN SEQRES 12 A 196 GLU GLU THR ILE LYS LYS ARG LEU GLU THR TYR TYR LYS SEQRES 13 A 196 ALA THR GLU PRO VAL ILE ALA PHE TYR GLU LYS ARG GLY SEQRES 14 A 196 ILE VAL ARG LYS VAL ASN ALA GLU GLY SER VAL ASP SER SEQRES 15 A 196 VAL PHE SER GLN VAL CYS THR HIS LEU ASP ALA LEU LEU SEQRES 16 A 196 ASN SEQRES 1 B 196 SER MET GLU GLU LYS LEU LYS LYS THR ASN ILE ILE PHE SEQRES 2 B 196 VAL VAL GLY GLY PRO GLY SER GLY LYS GLY THR GLN CYS SEQRES 3 B 196 GLU LYS ILE VAL GLN LYS TYR GLY TYR THR HIS LEU SER SEQRES 4 B 196 THR GLY ASP LEU LEU ARG SER GLU VAL SER SER GLY SER SEQRES 5 B 196 ALA ARG GLY LYS LYS LEU SER GLU ILE MET GLU LYS GLY SEQRES 6 B 196 GLN LEU VAL PRO LEU GLU THR VAL LEU ASP MET LEU ARG SEQRES 7 B 196 ASP ALA MET VAL ALA LYS VAL ASN THR SER LYS GLY PHE SEQRES 8 B 196 LEU ILE ASP GLY TYR PRO ARG GLU VAL GLN GLN GLY GLU SEQRES 9 B 196 GLU PHE GLU ARG ARG ILE GLY GLN PRO THR LEU LEU LEU SEQRES 10 B 196 TYR VAL ASP ALA GLY PRO GLU THR MET THR GLN ARG LEU SEQRES 11 B 196 LEU LYS ARG GLY GLU THR SER GLY ARG VAL ASP ASP ASN SEQRES 12 B 196 GLU GLU THR ILE LYS LYS ARG LEU GLU THR TYR TYR LYS SEQRES 13 B 196 ALA THR GLU PRO VAL ILE ALA PHE TYR GLU LYS ARG GLY SEQRES 14 B 196 ILE VAL ARG LYS VAL ASN ALA GLU GLY SER VAL ASP SER SEQRES 15 B 196 VAL PHE SER GLN VAL CYS THR HIS LEU ASP ALA LEU LEU SEQRES 16 B 196 ASN HET B4P A1195 53 HET MLI A1196 7 HET B4P B1196 53 HET MLI B1197 7 HETNAM B4P BIS(ADENOSINE)-5'-TETRAPHOSPHATE HETNAM MLI MALONATE ION FORMUL 3 B4P 2(C20 H28 N10 O19 P4) FORMUL 4 MLI 2(C3 H2 O4 2-) FORMUL 7 HOH *380(H2 O) HELIX 1 1 SER A 0 LYS A 6 1 7 HELIX 2 2 GLY A 20 GLY A 33 1 14 HELIX 3 3 THR A 39 SER A 49 1 11 HELIX 4 4 SER A 51 LYS A 63 1 13 HELIX 5 5 PRO A 68 VAL A 84 1 17 HELIX 6 6 GLU A 98 ILE A 109 1 12 HELIX 7 7 GLY A 121 GLU A 134 1 14 HELIX 8 8 ARG A 138 ASP A 141 5 4 HELIX 9 9 ASN A 142 THR A 157 1 16 HELIX 10 10 THR A 157 GLY A 168 1 12 HELIX 11 11 SER A 178 LEU A 194 1 17 HELIX 12 12 GLU B 3 LYS B 7 5 5 HELIX 13 13 GLY B 20 GLY B 33 1 14 HELIX 14 14 THR B 39 SER B 49 1 11 HELIX 15 15 SER B 51 LYS B 63 1 13 HELIX 16 16 PRO B 68 ALA B 82 1 15 HELIX 17 17 GLU B 98 ILE B 109 1 12 HELIX 18 18 GLY B 121 GLU B 134 1 14 HELIX 19 19 ARG B 138 ASP B 141 5 4 HELIX 20 20 ASN B 142 GLY B 168 1 27 HELIX 21 21 SER B 178 LEU B 194 1 17 SHEET 1 AA 5 THR A 35 SER A 38 0 SHEET 2 AA 5 PHE A 90 ASP A 93 1 O LEU A 91 N LEU A 37 SHEET 3 AA 5 ILE A 10 GLY A 15 1 O ILE A 11 N ILE A 92 SHEET 4 AA 5 LEU A 114 ASP A 119 1 O LEU A 114 N PHE A 12 SHEET 5 AA 5 VAL A 170 ASN A 174 1 O ARG A 171 N TYR A 117 SHEET 1 BA 5 THR B 35 SER B 38 0 SHEET 2 BA 5 PHE B 90 ASP B 93 1 O LEU B 91 N LEU B 37 SHEET 3 BA 5 ILE B 10 GLY B 15 1 O ILE B 11 N ILE B 92 SHEET 4 BA 5 LEU B 114 ASP B 119 1 O LEU B 114 N PHE B 12 SHEET 5 BA 5 VAL B 170 ASN B 174 1 O ARG B 171 N TYR B 117 CISPEP 1 TYR A 95 PRO A 96 0 1.23 CISPEP 2 TYR B 95 PRO B 96 0 -5.32 SITE 1 AC1 40 PRO A 17 GLY A 18 SER A 19 GLY A 20 SITE 2 AC1 40 LYS A 21 GLY A 22 THR A 23 THR A 39 SITE 3 AC1 40 GLY A 40 LEU A 43 ARG A 44 MET A 61 SITE 4 AC1 40 GLN A 65 VAL A 67 GLY A 94 TYR A 95 SITE 5 AC1 40 ARG A 97 GLN A 101 ARG A 128 ARG A 132 SITE 6 AC1 40 ARG A 138 ARG A 149 ARG A 167 GLY A 177 SITE 7 AC1 40 SER A 178 VAL A 179 HOH A2040 HOH A2065 SITE 8 AC1 40 HOH A2159 HOH A2179 HOH A2180 HOH A2181 SITE 9 AC1 40 HOH A2182 HOH A2183 HOH A2184 HOH A2185 SITE 10 AC1 40 HOH A2186 HOH A2187 HOH A2189 HOH A2190 SITE 1 AC2 7 GLU A 62 GLY A 137 ARG A 138 VAL A 139 SITE 2 AC2 7 ASP A 140 HOH A2191 HOH B2120 SITE 1 AC3 42 PRO B 17 GLY B 18 SER B 19 GLY B 20 SITE 2 AC3 42 LYS B 21 GLY B 22 THR B 23 THR B 39 SITE 3 AC3 42 GLY B 40 LEU B 43 ARG B 44 MET B 61 SITE 4 AC3 42 GLN B 65 VAL B 67 GLY B 94 TYR B 95 SITE 5 AC3 42 ARG B 97 GLN B 101 ARG B 128 ARG B 132 SITE 6 AC3 42 ARG B 138 ARG B 149 ARG B 167 GLY B 177 SITE 7 AC3 42 SER B 178 VAL B 179 HOH B2067 HOH B2070 SITE 8 AC3 42 HOH B2095 HOH B2175 HOH B2176 HOH B2177 SITE 9 AC3 42 HOH B2178 HOH B2179 HOH B2180 HOH B2181 SITE 10 AC3 42 HOH B2182 HOH B2183 HOH B2184 HOH B2185 SITE 11 AC3 42 HOH B2186 HOH B2187 SITE 1 AC4 4 SER B 58 MET B 61 ASP B 140 HOH B2189 CRYST1 62.535 69.998 88.558 90.00 90.00 90.00 P 21 21 21 8 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 0.015991 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014286 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011292 0.00000 MTRIX1 1 0.999920 -0.006110 -0.010960 -2.17906 1 MTRIX2 1 0.006080 0.999980 -0.003070 34.70399 1 MTRIX3 1 0.010980 0.003000 0.999940 -0.38201 1