10 20 30 40 50 60 70 80 1DLD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE (CHOH(D)-NAD+(A)) 25-JAN-95 1DLD
TITLE KNOWLEDGE-BASED MODELING OF THE D-LACTATE DEHYDROGENASE TITLE 2 THREE-DIMENSIONAL STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-LACTATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.28; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS DELBRUECKII SSP. BULGARICUS
KEYWDS OXIDOREDUCTASE (CHOH(D)-NAD+(A))
EXPDTA THEORETICAL MODEL
AUTHOR C.VINALS
REVDAT 1 31-MAR-95 1DLD 0
JRNL AUTH C.VINALS,X.DE BOLLE,E.DEPIEREUX,E.FEYTMANS JRNL TITL KNOWLEDGE-BASED MODELING OF THE D-LACTATE JRNL TITL 2 DEHYDROGENASE THREE-DIMENSIONAL STRUCTURE. JRNL REF PROTEINS V. 21 307 1995 JRNL REFN ASTM PSFGEY US ISSN 0887-3585
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.VINALS,E.DEPIEREUX,E.FEYTMANS REMARK 1 TITL PREDICTION OF STRUCTURALLY CONSERVED REGIONS OF REMARK 1 TITL 2 D-SPECIFIC HYDROXY ACID DEHYDROGENASES BY MULTIPLE REMARK 1 TITL 3 ALIGNMENT WITH FORMATE DEHYDROGENASE REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMM. V. 192 182 1993 REMARK 1 REFN ASTM BBRCA9 US ISSN 0006-291X
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1DLD COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 36 REMARK 36 TOPIC: STEREOCHEMISTRY REMARK 36 REMARK 36 SUBTOPIC: COVALENT BOND ANGLES (36.2) REMARK 36 REMARK 36 STANDARD TEXT: REMARK 36 REMARK 36 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 36 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 36 THAN 4*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 36 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 36 REMARK 36 STANDARD TABLE: REMARK 36 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(2X,A4,17X,F5.1) REMARK 36 REMARK 36 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 36 REMARK 36 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 36 REMARK 36 0 HIS 24 ND1 - CE1 - NE2 ANGL. DEV. = 11.7 DEGREES REMARK 36 0 HIS 110 ND1 - CE1 - NE2 ANGL. DEV. = 11.5 DEGREES REMARK 36 0 HIS 132 ND1 - CE1 - NE2 ANGL. DEV. = 11.8 DEGREES REMARK 36 0 HIS 156 ND1 - CE1 - NE2 ANGL. DEV. = 11.8 DEGREES REMARK 36 0 HIS 206 ND1 - CE1 - NE2 ANGL. DEV. = 11.4 DEGREES REMARK 36 0 HIS 297 ND1 - CE1 - NE2 ANGL. DEV. = 11.6 DEGREES REMARK 36 0 HIS 304 ND1 - CE1 - NE2 ANGL. DEV. = 11.6 DEGREES REMARK 36 REMARK 36 TOPIC: STEREOCHEMISTRY REMARK 36 REMARK 36 SUBTOPIC: TORSION ANGLES (36.4) REMARK 36 REMARK 36 STANDARD TEXT: REMARK 36 REMARK 36 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 36 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 36 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 36 REMARK 36 STANDARD TABLE: REMARK 36 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 36 REMARK 36 M RES CSSEQI PSI PHI REMARK 36 REMARK 36 0 ASP 22 68.64 -110.72 REMARK 36 0 TYR 31 69.47 -164.13 REMARK 36 0 VAL 52 -125.50 -117.14 REMARK 36 0 ASP 68 100.92 161.96 REMARK 36 0 GLN 121 148.40 80.32 REMARK 36 0 ASP 122 -138.63 -100.15 REMARK 36 0 ALA 124 66.22 -60.04 REMARK 36 0 ASP 133 -116.42 -96.63 REMARK 36 0 ARG 142 -142.98 -116.89 REMARK 36 0 GLU 143 64.56 -124.00 REMARK 36 0 GLU 265 -150.85 -97.51 REMARK 36 0 LEU 283 67.00 135.82
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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 M RES CSSEQI PSI PHI REMARK 500 ASP A 22 -110.72 68.64 REMARK 500 ASP A 68 161.96 100.92 REMARK 500 GLN A 121 80.32 148.40 REMARK 500 ALA A 124 -60.04 66.22 REMARK 500 LEU A 283 135.82 67.00 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 ILE A 9 ARG A 10 149.32 REMARK 500 GLN A 54 GLN A 55 144.24 REMARK 500 ASP A 57 TYR A 58 133.65 REMARK 500 TYR A 58 THR A 59 -136.81 REMARK 500 LEU A 134 ARG A 135 148.12 REMARK 500 TYR A 188 TYR A 189 -145.95 REMARK 500 ASN A 291 VAL A 292 -148.67 REMARK 500 THR A 295 PRO A 296 146.77
REMARK 999 REMARK 999 DATABASE USED: PIR REMARK 999 DATABASE ENTRY NAME: S17556 REMARK 999 AUTHORS: N. BERNARD, T. FERAIN, D. GARMYN, P. HOLS, REMARK 999 J. DELCOUR REMARK 999 JOURNAL: FEBS LETT. (1991) 290:61-64 REMARK 999 TITLE: CLONING OF THE D-LACTATE DEHYDROGENASE GENE FROM REMARK 999 LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS BY REMARK 999 COMPLEMENTATION IN ESCHERICHIA COLI. REMARK 999 CROSS REFERENCE TO SEQUENCE DATABASE REMARK 999 SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME REMARK 999 LDHD_LACDE REMARK 999 REMARK 999 N-TERMINUS RESIDUES NOT FOUND IN THE SEQUENCE DATABASE REMARK 999 ENTRY REMARK 999 MET 1 REMARK 999 REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: LDHD_LACDE REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 ALA 40 VAL 41 REMARK 999 ARG 116 ALA 117 REMARK 999 ALA 121 ASP 122 REMARK 999 VAL 151 ILE 152 REMARK 999 ALA 173 THR 174 REMARK 999 LYS 219 GLU 220 REMARK 999 VAL 253 ILE 254 REMARK 999 VAL 267 ILE 268 REMARK 999 ARG 272 TRP 273 REMARK 999 REMARK 999 THE OBSERVED DISCREPANCY BETWEEN THE SEQUENCE OBTAINED FROM REMARK 999 THE ATOMIC COORDINATES AND THE SWISSPROT SEQUENCE REMARK 999 LDHD_LACDE IS DUE TO THE FACT THAT TWO AUTHORS PUBLISHED REMARK 999 THE SAME SEQUENCE SIMULTANEOUSLY, AND THESE DIFFER IN A REMARK 999 NUMBER OF POSITIONS. THE 3D MODEL WAS BUILT USING THE REMARK 999 SEQUENCE S17556 (PIR) FROM BERNARD ET AL.,THE SOURCE OF REMARK 999 LDHD_LACDE BEING FROM KOCHHAR ET AL.
DBREF 1DLD A 1 333 EMBL X60220 CAA42781 1 333
SEQRES 1 A 333 MET THR LYS ILE PHE ALA TYR ALA ILE ARG GLU ASP GLU SEQRES 2 A 333 LYS PRO PHE LEU LYS GLU TRP GLU ASP ALA HIS LYS ASP SEQRES 3 A 333 VAL GLU VAL GLU TYR THR ASP LYS LEU LEU THR PRO GLU SEQRES 4 A 333 THR VAL ALA LEU ALA LYS GLY ALA ASP GLY VAL VAL VAL SEQRES 5 A 333 TYR GLN GLN LEU ASP TYR THR ALA GLU THR LEU GLN ALA SEQRES 6 A 333 LEU ALA ASP ASN GLY ILE THR LYS MET SER LEU ARG ASN SEQRES 7 A 333 VAL GLY VAL ASP ASN ILE ASP MET ALA LYS ALA LYS GLU SEQRES 8 A 333 LEU GLY PHE GLN ILE THR ASN VAL PRO VAL TYR SER PRO SEQRES 9 A 333 ASN ALA ILE ALA GLU HIS ALA ALA ILE GLN ALA ALA ALA SEQRES 10 A 333 ILE LEU ARG GLN ASP LYS ALA MET ASP GLU LYS VAL ALA SEQRES 11 A 333 ARG HIS ASP LEU ARG TRP ALA PRO THR ILE GLY ARG GLU SEQRES 12 A 333 VAL ARG ASP GLN VAL VAL GLY VAL ILE GLY THR GLY HIS SEQRES 13 A 333 ILE GLY GLN VAL PHE MET GLN ILE MET GLU GLY PHE GLY SEQRES 14 A 333 ALA LYS VAL ILE THR TYR ASP ILE PHE ARG ASN PRO GLU SEQRES 15 A 333 LEU GLU LYS LYS GLY TYR TYR VAL ASP SER LEU ASP ASP SEQRES 16 A 333 LEU TYR LYS GLN ALA ASP VAL ILE SER LEU HIS VAL PRO SEQRES 17 A 333 ASP VAL PRO ALA ASN VAL HIS MET ILE ASN ASP GLU SER SEQRES 18 A 333 ILE ALA LYS MET LYS GLN ASP VAL VAL ILE VAL ASN VAL SEQRES 19 A 333 SER ARG GLY PRO LEU VAL ASP THR ASP ALA VAL ILE ARG SEQRES 20 A 333 GLY LEU ASP SER GLY LYS ILE PHE GLY TYR ALA MET ASP SEQRES 21 A 333 VAL TYR GLU GLY GLU VAL GLY ILE PHE ASN GLU ASP TRP SEQRES 22 A 333 GLU GLY LYS GLU PHE PRO ASP ALA ARG LEU ALA ASP LEU SEQRES 23 A 333 ILE ALA ARG PRO ASN VAL LEU VAL THR PRO HIS THR ALA SEQRES 24 A 333 PHE TYR THR THR HIS ALA VAL ARG ASN MET VAL VAL LYS SEQRES 25 A 333 ALA PHE ASP ASN ASN LEU GLU LEU VAL GLU GLY LYS GLU SEQRES 26 A 333 ALA GLU THR PRO VAL LYS VAL GLY
FTNOTE 1 ILE 9 - ARG 10 OMEGA = 149.32 PEPTIDE BOND DEVIATES FTNOTE 1 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 2 GLN 54 - GLN 55 OMEGA = 144.24 PEPTIDE BOND DEVIATES FTNOTE 2 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 3 ASP 57 - TYR 58 OMEGA = 133.23 PEPTIDE BOND DEVIATES FTNOTE 3 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 4 TYR 58 - THR 59 OMEGA = 229.51 PEPTIDE BOND DEVIATES FTNOTE 4 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 5 LEU 134 - ARG 135 OMEGA = 148.12 PEPTIDE BOND DEVIATES FTNOTE 5 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 6 ARG 142 - GLU 143 OMEGA = 148.23 PEPTIDE BOND DEVIATES FTNOTE 6 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 7 TYR 188 - TYR 189 OMEGA = 214.05 PEPTIDE BOND DEVIATES FTNOTE 7 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 8 ASN 291 - VAL 292 OMEGA = 211.33 PEPTIDE BOND DEVIATES FTNOTE 8 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 9 THR 295 - PRO 296 OMEGA = 146.77 PEPTIDE BOND DEVIATES FTNOTE 9 SIGNIFICANTLY FROM TRANS CONFORMATION
HET NAD 394 71 HET PYR 402 9
HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PYR PYRUVIC ACID
FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 PYR C3 H4 O3
HELIX 1 1 LYS A 14 GLU A 19 1 6 HELIX 2 2 LEU A 35 ALA A 42 1 8 HELIX 3 3 ALA A 60 GLN A 64 1 5 HELIX 4 4 VAL A 81 ASN A 83 5 3 HELIX 5 5 MET A 86 LEU A 92 1 7 HELIX 6 6 PRO A 104 ILE A 118 1 15 HELIX 7 7 GLY A 158 PHE A 168 1 11 HELIX 8 8 LEU A 193 GLN A 199 1 7 HELIX 9 9 ASP A 219 LYS A 224 1 6 HELIX 10 10 THR A 242 SER A 251 1 10 HELIX 11 11 THR A 303 GLU A 322 1 20
SHEET 1 A 4 ILE A 4 ALA A 6 0 SHEET 2 A 4 LYS A 45 ASP A 48 1 N LYS A 45 O PHE A 5 SHEET 3 A 4 LYS A 73 LEU A 76 1 N LYS A 73 O GLY A 46 SHEET 4 A 4 GLN A 95 THR A 97 1 N GLN A 95 O MET A 74 SHEET 1 B 3 ALA A 170 TYR A 175 0 SHEET 2 B 3 GLN A 147 ILE A 152 1 N GLN A 147 O LYS A 171 SHEET 3 B 3 VAL A 202 LEU A 205 1 N VAL A 202 O GLY A 150 SHEET 1 C 3 ILE A 231 ASN A 233 0 SHEET 2 C 3 TYR A 257 MET A 259 1 N ALA A 258 O ILE A 231 SHEET 3 C 3 VAL A 292 VAL A 294 1 N LEU A 293 O TYR A 257
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000