HEADER HYDROLASE 30-MAR-20 7BSK TITLE CRYSTAL STRUCTURE OF HUMAN ME2 R67Q MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT MALIC ENZYME, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NAD-ME,MALIC ENZYME 2; COMPND 5 EC: 1.1.1.38; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ME2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS MALATE DEHYDROGENASE, NAD-DEPENDENT MALIC ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.L.CHEN,S.C.TAI,H.C.HUNG,M.C.HO REVDAT 3 29-NOV-23 7BSK 1 REMARK REVDAT 2 24-FEB-21 7BSK 1 JRNL REVDAT 1 10-FEB-21 7BSK 0 JRNL AUTH J.Y.HSIEH,H.P.YANG,S.K.TEWARY,H.C.CHENG,Y.L.LIU,S.C.TAI, JRNL AUTH 2 W.L.CHEN,C.H.HSU,T.J.HUANG,C.J.CHOU,Y.N.HUANG,C.T.PENG, JRNL AUTH 3 M.C.HO,G.Y.LIU,H.C.HUNG JRNL TITL SINGLE NUCLEOTIDE VARIANTS LEAD TO DYSREGULATION OF THE JRNL TITL 2 HUMAN MITOCHONDRIAL NAD(P) + -DEPENDENT MALIC ENZYME. JRNL REF ISCIENCE V. 24 02034 2021 JRNL REFN ESSN 2589-0042 JRNL PMID 33554057 JRNL DOI 10.1016/J.ISCI.2021.102034 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 38081 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1709 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 176 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.03000 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): 1.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.360 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.281 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.293 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8999 ; 0.004 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 8420 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12215 ; 1.378 ; 1.679 REMARK 3 BOND ANGLES OTHERS (DEGREES): 19544 ; 1.178 ; 1.588 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1092 ; 6.585 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 456 ;32.844 ;22.149 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1546 ;20.341 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 60 ;16.572 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1188 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9922 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1890 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7BSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-20. REMARK 100 THE DEPOSITION ID IS D_1300016409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44503 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.70800 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: PHENIX REMARK 200 STARTING MODEL: 1EFL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG20000 6.575% MPD(V/V) 5% MES REMARK 280 (PH=6.5), PH 6.5, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,-Z 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 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 58.92400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 95.70550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 58.92400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 95.70550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 83810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 117.84800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 382.82200 REMARK 350 BIOMT3 2 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 MET A 19 REMARK 465 HIS A 20 REMARK 465 ILE A 21 REMARK 465 LYS A 22 REMARK 465 LEU A 566 REMARK 465 PRO A 567 REMARK 465 ASP A 568 REMARK 465 VAL A 569 REMARK 465 TYR A 570 REMARK 465 GLU A 571 REMARK 465 TRP A 572 REMARK 465 PRO A 573 REMARK 465 GLU A 574 REMARK 465 SER A 575 REMARK 465 ALA A 576 REMARK 465 SER A 577 REMARK 465 SER A 578 REMARK 465 PRO A 579 REMARK 465 PRO A 580 REMARK 465 VAL A 581 REMARK 465 ILE A 582 REMARK 465 THR A 583 REMARK 465 GLU A 584 REMARK 465 MET B 19 REMARK 465 HIS B 20 REMARK 465 ILE B 21 REMARK 465 LYS B 22 REMARK 465 GLU B 574 REMARK 465 SER B 575 REMARK 465 ALA B 576 REMARK 465 SER B 577 REMARK 465 SER B 578 REMARK 465 PRO B 579 REMARK 465 PRO B 580 REMARK 465 VAL B 581 REMARK 465 ILE B 582 REMARK 465 THR B 583 REMARK 465 GLU B 584 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 OD1 ASP A 279 O HOH A 701 2.05 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 ARG A 91 -44.73 -133.52 REMARK 500 TYR A 112 -161.22 -122.26 REMARK 500 THR A 113 128.20 -38.13 REMARK 500 ILE A 280 -66.36 -97.04 REMARK 500 ASP A 345 -154.16 -116.83 REMARK 500 LYS A 385 74.48 32.13 REMARK 500 PRO A 448 53.86 -90.82 REMARK 500 TYR B 112 -159.76 -122.81 REMARK 500 LEU B 169 -58.10 -140.75 REMARK 500 LYS B 300 118.87 -38.12 REMARK 500 ASP B 345 -164.36 -100.77 REMARK 500 VAL B 392 44.14 -141.76 REMARK 500 PRO B 422 -168.59 -76.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE B 309 LEU B 310 149.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 602 DBREF 7BSK A 20 584 UNP P23368 MAOM_HUMAN 20 584 DBREF 7BSK B 20 584 UNP P23368 MAOM_HUMAN 20 584 SEQADV 7BSK MET A 19 UNP P23368 INITIATING METHIONINE SEQADV 7BSK GLN A 67 UNP P23368 ARG 67 ENGINEERED MUTATION SEQADV 7BSK MET B 19 UNP P23368 INITIATING METHIONINE SEQADV 7BSK GLN B 67 UNP P23368 ARG 67 ENGINEERED MUTATION SEQRES 1 A 566 MET HIS ILE LYS GLU LYS GLY LYS PRO LEU MET LEU ASN SEQRES 2 A 566 PRO ARG THR ASN LYS GLY MET ALA PHE THR LEU GLN GLU SEQRES 3 A 566 ARG GLN MET LEU GLY LEU GLN GLY LEU LEU PRO PRO LYS SEQRES 4 A 566 ILE GLU THR GLN ASP ILE GLN ALA LEU GLN PHE HIS ARG SEQRES 5 A 566 ASN LEU LYS LYS MET THR SER PRO LEU GLU LYS TYR ILE SEQRES 6 A 566 TYR ILE MET GLY ILE GLN GLU ARG ASN GLU LYS LEU PHE SEQRES 7 A 566 TYR ARG ILE LEU GLN ASP ASP ILE GLU SER LEU MET PRO SEQRES 8 A 566 ILE VAL TYR THR PRO THR VAL GLY LEU ALA CYS SER GLN SEQRES 9 A 566 TYR GLY HIS ILE PHE ARG ARG PRO LYS GLY LEU PHE ILE SEQRES 10 A 566 SER ILE SER ASP ARG GLY HIS VAL ARG SER ILE VAL ASP SEQRES 11 A 566 ASN TRP PRO GLU ASN HIS VAL LYS ALA VAL VAL VAL THR SEQRES 12 A 566 ASP GLY GLU ARG ILE LEU GLY LEU GLY ASP LEU GLY VAL SEQRES 13 A 566 TYR GLY MET GLY ILE PRO VAL GLY LYS LEU CYS LEU TYR SEQRES 14 A 566 THR ALA CYS ALA GLY ILE ARG PRO ASP ARG CYS LEU PRO SEQRES 15 A 566 VAL CYS ILE ASP VAL GLY THR ASP ASN ILE ALA LEU LEU SEQRES 16 A 566 LYS ASP PRO PHE TYR MET GLY LEU TYR GLN LYS ARG ASP SEQRES 17 A 566 ARG THR GLN GLN TYR ASP ASP LEU ILE ASP GLU PHE MET SEQRES 18 A 566 LYS ALA ILE THR ASP ARG TYR GLY ARG ASN THR LEU ILE SEQRES 19 A 566 GLN PHE GLU ASP PHE GLY ASN HIS ASN ALA PHE ARG PHE SEQRES 20 A 566 LEU ARG LYS TYR ARG GLU LYS TYR CYS THR PHE ASN ASP SEQRES 21 A 566 ASP ILE GLN GLY THR ALA ALA VAL ALA LEU ALA GLY LEU SEQRES 22 A 566 LEU ALA ALA GLN LYS VAL ILE SER LYS PRO ILE SER GLU SEQRES 23 A 566 HIS LYS ILE LEU PHE LEU GLY ALA GLY GLU ALA ALA LEU SEQRES 24 A 566 GLY ILE ALA ASN LEU ILE VAL MET SER MET VAL GLU ASN SEQRES 25 A 566 GLY LEU SER GLU GLN GLU ALA GLN LYS LYS ILE TRP MET SEQRES 26 A 566 PHE ASP LYS TYR GLY LEU LEU VAL LYS GLY ARG LYS ALA SEQRES 27 A 566 LYS ILE ASP SER TYR GLN GLU PRO PHE THR HIS SER ALA SEQRES 28 A 566 PRO GLU SER ILE PRO ASP THR PHE GLU ASP ALA VAL ASN SEQRES 29 A 566 ILE LEU LYS PRO SER THR ILE ILE GLY VAL ALA GLY ALA SEQRES 30 A 566 GLY ARG LEU PHE THR PRO ASP VAL ILE ARG ALA MET ALA SEQRES 31 A 566 SER ILE ASN GLU ARG PRO VAL ILE PHE ALA LEU SER ASN SEQRES 32 A 566 PRO THR ALA GLN ALA GLU CYS THR ALA GLU GLU ALA TYR SEQRES 33 A 566 THR LEU THR GLU GLY ARG CYS LEU PHE ALA SER GLY SER SEQRES 34 A 566 PRO PHE GLY PRO VAL LYS LEU THR ASP GLY ARG VAL PHE SEQRES 35 A 566 THR PRO GLY GLN GLY ASN ASN VAL TYR ILE PHE PRO GLY SEQRES 36 A 566 VAL ALA LEU ALA VAL ILE LEU CYS ASN THR ARG HIS ILE SEQRES 37 A 566 SER ASP SER VAL PHE LEU GLU ALA ALA LYS ALA LEU THR SEQRES 38 A 566 SER GLN LEU THR ASP GLU GLU LEU ALA GLN GLY ARG LEU SEQRES 39 A 566 TYR PRO PRO LEU ALA ASN ILE GLN GLU VAL SER ILE ASN SEQRES 40 A 566 ILE ALA ILE LYS VAL THR GLU TYR LEU TYR ALA ASN LYS SEQRES 41 A 566 MET ALA PHE ARG TYR PRO GLU PRO GLU ASP LYS ALA LYS SEQRES 42 A 566 TYR VAL LYS GLU ARG THR TRP ARG SER GLU TYR ASP SER SEQRES 43 A 566 LEU LEU PRO ASP VAL TYR GLU TRP PRO GLU SER ALA SER SEQRES 44 A 566 SER PRO PRO VAL ILE THR GLU SEQRES 1 B 566 MET HIS ILE LYS GLU LYS GLY LYS PRO LEU MET LEU ASN SEQRES 2 B 566 PRO ARG THR ASN LYS GLY MET ALA PHE THR LEU GLN GLU SEQRES 3 B 566 ARG GLN MET LEU GLY LEU GLN GLY LEU LEU PRO PRO LYS SEQRES 4 B 566 ILE GLU THR GLN ASP ILE GLN ALA LEU GLN PHE HIS ARG SEQRES 5 B 566 ASN LEU LYS LYS MET THR SER PRO LEU GLU LYS TYR ILE SEQRES 6 B 566 TYR ILE MET GLY ILE GLN GLU ARG ASN GLU LYS LEU PHE SEQRES 7 B 566 TYR ARG ILE LEU GLN ASP ASP ILE GLU SER LEU MET PRO SEQRES 8 B 566 ILE VAL TYR THR PRO THR VAL GLY LEU ALA CYS SER GLN SEQRES 9 B 566 TYR GLY HIS ILE PHE ARG ARG PRO LYS GLY LEU PHE ILE SEQRES 10 B 566 SER ILE SER ASP ARG GLY HIS VAL ARG SER ILE VAL ASP SEQRES 11 B 566 ASN TRP PRO GLU ASN HIS VAL LYS ALA VAL VAL VAL THR SEQRES 12 B 566 ASP GLY GLU ARG ILE LEU GLY LEU GLY ASP LEU GLY VAL SEQRES 13 B 566 TYR GLY MET GLY ILE PRO VAL GLY LYS LEU CYS LEU TYR SEQRES 14 B 566 THR ALA CYS ALA GLY ILE ARG PRO ASP ARG CYS LEU PRO SEQRES 15 B 566 VAL CYS ILE ASP VAL GLY THR ASP ASN ILE ALA LEU LEU SEQRES 16 B 566 LYS ASP PRO PHE TYR MET GLY LEU TYR GLN LYS ARG ASP SEQRES 17 B 566 ARG THR GLN GLN TYR ASP ASP LEU ILE ASP GLU PHE MET SEQRES 18 B 566 LYS ALA ILE THR ASP ARG TYR GLY ARG ASN THR LEU ILE SEQRES 19 B 566 GLN PHE GLU ASP PHE GLY ASN HIS ASN ALA PHE ARG PHE SEQRES 20 B 566 LEU ARG LYS TYR ARG GLU LYS TYR CYS THR PHE ASN ASP SEQRES 21 B 566 ASP ILE GLN GLY THR ALA ALA VAL ALA LEU ALA GLY LEU SEQRES 22 B 566 LEU ALA ALA GLN LYS VAL ILE SER LYS PRO ILE SER GLU SEQRES 23 B 566 HIS LYS ILE LEU PHE LEU GLY ALA GLY GLU ALA ALA LEU SEQRES 24 B 566 GLY ILE ALA ASN LEU ILE VAL MET SER MET VAL GLU ASN SEQRES 25 B 566 GLY LEU SER GLU GLN GLU ALA GLN LYS LYS ILE TRP MET SEQRES 26 B 566 PHE ASP LYS TYR GLY LEU LEU VAL LYS GLY ARG LYS ALA SEQRES 27 B 566 LYS ILE ASP SER TYR GLN GLU PRO PHE THR HIS SER ALA SEQRES 28 B 566 PRO GLU SER ILE PRO ASP THR PHE GLU ASP ALA VAL ASN SEQRES 29 B 566 ILE LEU LYS PRO SER THR ILE ILE GLY VAL ALA GLY ALA SEQRES 30 B 566 GLY ARG LEU PHE THR PRO ASP VAL ILE ARG ALA MET ALA SEQRES 31 B 566 SER ILE ASN GLU ARG PRO VAL ILE PHE ALA LEU SER ASN SEQRES 32 B 566 PRO THR ALA GLN ALA GLU CYS THR ALA GLU GLU ALA TYR SEQRES 33 B 566 THR LEU THR GLU GLY ARG CYS LEU PHE ALA SER GLY SER SEQRES 34 B 566 PRO PHE GLY PRO VAL LYS LEU THR ASP GLY ARG VAL PHE SEQRES 35 B 566 THR PRO GLY GLN GLY ASN ASN VAL TYR ILE PHE PRO GLY SEQRES 36 B 566 VAL ALA LEU ALA VAL ILE LEU CYS ASN THR ARG HIS ILE SEQRES 37 B 566 SER ASP SER VAL PHE LEU GLU ALA ALA LYS ALA LEU THR SEQRES 38 B 566 SER GLN LEU THR ASP GLU GLU LEU ALA GLN GLY ARG LEU SEQRES 39 B 566 TYR PRO PRO LEU ALA ASN ILE GLN GLU VAL SER ILE ASN SEQRES 40 B 566 ILE ALA ILE LYS VAL THR GLU TYR LEU TYR ALA ASN LYS SEQRES 41 B 566 MET ALA PHE ARG TYR PRO GLU PRO GLU ASP LYS ALA LYS SEQRES 42 B 566 TYR VAL LYS GLU ARG THR TRP ARG SER GLU TYR ASP SER SEQRES 43 B 566 LEU LEU PRO ASP VAL TYR GLU TRP PRO GLU SER ALA SER SEQRES 44 B 566 SER PRO PRO VAL ILE THR GLU HET NAD A 601 44 HET NAD A 602 44 HET NAD B 601 44 HET NAD B 602 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 NAD 4(C21 H27 N7 O14 P2) FORMUL 7 HOH *93(H2 O) HELIX 1 AA1 GLY A 25 ASN A 31 1 7 HELIX 2 AA2 LYS A 36 PHE A 40 5 5 HELIX 3 AA3 THR A 41 LEU A 48 1 8 HELIX 4 AA4 THR A 60 MET A 75 1 16 HELIX 5 AA5 SER A 77 GLU A 90 1 14 HELIX 6 AA6 ASN A 92 ASP A 103 1 12 HELIX 7 AA7 ASP A 103 TYR A 112 1 10 HELIX 8 AA8 PRO A 114 GLN A 122 1 9 HELIX 9 AA9 SER A 138 ARG A 140 5 3 HELIX 10 AB1 HIS A 142 ASN A 149 1 8 HELIX 11 AB2 LEU A 172 GLY A 176 5 5 HELIX 12 AB3 MET A 177 GLY A 192 1 16 HELIX 13 AB4 ARG A 194 ASP A 196 5 3 HELIX 14 AB5 ASN A 209 LYS A 214 1 6 HELIX 15 AB6 THR A 228 GLY A 247 1 20 HELIX 16 AB7 GLY A 258 ARG A 270 1 13 HELIX 17 AB8 ILE A 280 SER A 299 1 20 HELIX 18 AB9 PRO A 301 HIS A 305 5 5 HELIX 19 AC1 GLY A 313 ASN A 330 1 18 HELIX 20 AC2 SER A 333 LYS A 339 1 7 HELIX 21 AC3 GLN A 362 THR A 366 5 5 HELIX 22 AC4 THR A 376 LYS A 385 1 10 HELIX 23 AC5 THR A 400 ASN A 411 1 12 HELIX 24 AC6 PRO A 422 ALA A 426 5 5 HELIX 25 AC7 THR A 429 LEU A 436 1 8 HELIX 26 AC8 ASN A 466 TYR A 469 5 4 HELIX 27 AC9 ILE A 470 CYS A 481 1 12 HELIX 28 AD1 SER A 487 GLN A 501 1 15 HELIX 29 AD2 THR A 503 GLN A 509 1 7 HELIX 30 AD3 PRO A 515 ALA A 517 5 3 HELIX 31 AD4 ASN A 518 ASN A 537 1 20 HELIX 32 AD5 ASP A 548 GLU A 555 1 8 HELIX 33 AD6 LYS B 26 ASN B 31 1 6 HELIX 34 AD7 LYS B 36 PHE B 40 5 5 HELIX 35 AD8 THR B 41 LEU B 48 1 8 HELIX 36 AD9 THR B 60 LYS B 73 1 14 HELIX 37 AE1 SER B 77 GLU B 90 1 14 HELIX 38 AE2 ASN B 92 ASP B 103 1 12 HELIX 39 AE3 ASP B 103 TYR B 112 1 10 HELIX 40 AE4 PRO B 114 ARG B 128 1 15 HELIX 41 AE5 SER B 138 ARG B 140 5 3 HELIX 42 AE6 HIS B 142 ASP B 148 1 7 HELIX 43 AE7 LEU B 172 GLY B 176 5 5 HELIX 44 AE8 MET B 177 GLY B 192 1 16 HELIX 45 AE9 ARG B 194 ASP B 196 5 3 HELIX 46 AF1 ASN B 209 LYS B 214 1 6 HELIX 47 AF2 THR B 228 GLY B 247 1 20 HELIX 48 AF3 GLY B 258 ARG B 270 1 13 HELIX 49 AF4 ILE B 280 ILE B 298 1 19 HELIX 50 AF5 PRO B 301 HIS B 305 5 5 HELIX 51 AF6 GLY B 313 GLU B 329 1 17 HELIX 52 AF7 SER B 333 LYS B 339 1 7 HELIX 53 AF8 GLN B 362 THR B 366 5 5 HELIX 54 AF9 THR B 376 LYS B 385 1 10 HELIX 55 AG1 THR B 400 ASN B 411 1 12 HELIX 56 AG2 PRO B 422 ALA B 426 5 5 HELIX 57 AG3 THR B 429 LEU B 436 1 8 HELIX 58 AG4 ASN B 466 TYR B 469 5 4 HELIX 59 AG5 ILE B 470 CYS B 481 1 12 HELIX 60 AG6 SER B 487 SER B 500 1 14 HELIX 61 AG7 THR B 503 GLN B 509 1 7 HELIX 62 AG8 PRO B 515 ALA B 517 5 3 HELIX 63 AG9 ASN B 518 ASN B 537 1 20 HELIX 64 AH1 ASP B 548 GLU B 555 1 8 SHEET 1 AA1 5 LEU A 133 SER A 136 0 SHEET 2 AA1 5 CYS A 198 ASP A 204 1 O CYS A 202 N LEU A 133 SHEET 3 AA1 5 ALA A 157 THR A 161 1 N THR A 161 O ILE A 203 SHEET 4 AA1 5 LEU A 251 PHE A 254 1 O LEU A 251 N VAL A 158 SHEET 5 AA1 5 CYS A 274 ASN A 277 1 O CYS A 274 N ILE A 252 SHEET 1 AA2 7 GLY A 348 LEU A 349 0 SHEET 2 AA2 7 ILE A 341 ASP A 345 -1 N ASP A 345 O GLY A 348 SHEET 3 AA2 7 ILE A 307 LEU A 310 1 N ILE A 307 O TRP A 342 SHEET 4 AA2 7 THR A 388 GLY A 391 1 O ILE A 390 N LEU A 310 SHEET 5 AA2 7 VAL A 415 ALA A 418 1 O PHE A 417 N GLY A 391 SHEET 6 AA2 7 LEU A 442 SER A 445 1 O LEU A 442 N ILE A 416 SHEET 7 AA2 7 GLY A 463 GLN A 464 1 O GLY A 463 N SER A 445 SHEET 1 AA3 2 VAL A 452 LYS A 453 0 SHEET 2 AA3 2 VAL A 459 PHE A 460 -1 O PHE A 460 N VAL A 452 SHEET 1 AA4 4 LEU B 133 SER B 136 0 SHEET 2 AA4 4 CYS B 198 ASP B 204 1 O CYS B 202 N LEU B 133 SHEET 3 AA4 4 ALA B 157 THR B 161 1 N THR B 161 O ILE B 203 SHEET 4 AA4 4 LEU B 251 PHE B 254 1 O LEU B 251 N VAL B 158 SHEET 1 AA5 7 GLY B 348 LEU B 349 0 SHEET 2 AA5 7 ILE B 341 ASP B 345 -1 N ASP B 345 O GLY B 348 SHEET 3 AA5 7 ILE B 307 LEU B 310 1 N PHE B 309 O TRP B 342 SHEET 4 AA5 7 THR B 388 GLY B 391 1 O THR B 388 N LEU B 308 SHEET 5 AA5 7 VAL B 415 ALA B 418 1 O PHE B 417 N GLY B 391 SHEET 6 AA5 7 LEU B 442 SER B 445 1 O ALA B 444 N ALA B 418 SHEET 7 AA5 7 GLY B 463 GLN B 464 1 O GLY B 463 N SER B 445 SHEET 1 AA6 2 VAL B 452 LYS B 453 0 SHEET 2 AA6 2 VAL B 459 PHE B 460 -1 O PHE B 460 N VAL B 452 CISPEP 1 THR A 113 PRO A 114 0 -1.06 CISPEP 2 TYR A 543 PRO A 544 0 14.90 CISPEP 3 THR B 113 PRO B 114 0 0.26 CISPEP 4 ASN B 421 PRO B 422 0 -6.12 CISPEP 5 TYR B 543 PRO B 544 0 7.01 SITE 1 AC1 16 ASN A 259 ASP A 279 THR A 283 GLY A 311 SITE 2 AC1 16 ALA A 312 GLY A 313 ASP A 345 LYS A 346 SITE 3 AC1 16 VAL A 392 ALA A 393 GLY A 394 LEU A 398 SITE 4 AC1 16 LEU A 419 ASN A 421 PRO A 422 LYS B 453 SITE 1 AC2 14 LYS A 156 GLY A 192 ILE A 193 ARG A 194 SITE 2 AC2 14 ARG A 197 ILE A 479 LEU A 480 ASN A 482 SITE 3 AC2 14 ARG A 542 TYR A 552 GLU A 555 ARG A 556 SITE 4 AC2 14 TRP A 558 HOH A 707 SITE 1 AC3 17 LYS A 453 GLY A 457 ARG B 165 LEU B 167 SITE 2 AC3 17 ASN B 259 PHE B 263 GLY B 311 ALA B 312 SITE 3 AC3 17 GLY B 313 ASP B 345 LYS B 346 VAL B 392 SITE 4 AC3 17 ALA B 393 LEU B 398 SER B 420 ASN B 421 SITE 5 AC3 17 PRO B 422 SITE 1 AC4 12 ARG A 245 LYS B 156 GLY B 192 ILE B 193 SITE 2 AC4 12 ARG B 194 ARG B 197 ILE B 479 LEU B 480 SITE 3 AC4 12 ASN B 482 ARG B 542 ARG B 556 TRP B 558 CRYST1 117.848 191.411 58.909 90.00 90.00 90.00 P 21 21 2 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 0.008486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016975 0.00000