SMTL ID : 1geg.2 (1 other biounit)

CRYATAL STRUCTURE ANALYSIS OF MESO-2,3-BUTANEDIOL DEHYDROGENASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 4 residues within 4Å: Chain A: R.63, D.64, F.67, E.123 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.64 GLC.4: 2 residues within 4Å: Chain B: F.67, E.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.127 Water bridges: B:R.63 Salt bridges: B:R.63 GLC.7: 4 residues within 4Å: Chain C: R.63, D.64, F.67, E.123 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.64 Water bridges: C:D.64, C:A.68 GLC.11: 4 residues within 4Å: Chain D: R.63, D.64, F.67, E.123 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.64 Salt bridges: D:R.63

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 28 residues within 4Å: Chain A: G.9, Q.12, G.13, I.14, D.33, Y.34, N.35, V.58, D.59, V.60, N.86, A.87, G.88, I.109, A.137, C.138, S.139, Y.152, K.156, P.182, G.183, I.184, V.185, T.187, P.188, M.189, W.190 Ligands: BME.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.182 Hydrogen bonds: A:Q.12, A:Q.12, A:I.14, A:Y.34, A:D.59, A:V.60, A:N.86, A:Y.152, A:K.156, A:V.185, A:V.185, A:T.187, A:M.189, A:W.190 NAD.5: 28 residues within 4Å: Chain B: G.9, Q.12, G.13, I.14, D.33, Y.34, N.35, V.58, D.59, V.60, N.86, A.87, G.88, I.109, A.137, C.138, S.139, Y.152, K.156, P.182, G.183, I.184, V.185, T.187, P.188, M.189, W.190 Ligands: BME.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.182, B:V.185 Hydrogen bonds: B:G.9, B:G.11, B:Q.12, B:Q.12, B:I.14, B:Y.34, B:D.59, B:V.60, B:N.86, B:K.156, B:V.185, B:V.185, B:T.187, B:T.187, B:M.189, B:W.190 Water bridges: B:Q.12, B:T.38 NAD.9: 28 residues within 4Å: Chain C: G.9, Q.12, G.13, I.14, D.33, Y.34, N.35, V.58, D.59, V.60, N.86, A.87, G.88, I.109, A.137, C.138, S.139, Y.152, K.156, P.182, G.183, I.184, V.185, T.187, P.188, M.189, W.190 Ligands: BME.10 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.182, C:V.185 Hydrogen bonds: C:G.9, C:G.11, C:Q.12, C:Q.12, C:I.14, C:G.15, C:Y.34, C:D.59, C:D.59, C:V.60, C:N.86, C:K.156, C:V.185, C:V.185, C:T.187, C:M.189, C:W.190 Water bridges: C:Q.12, C:N.35, C:T.38 NAD.13: 28 residues within 4Å: Chain D: G.9, Q.12, G.13, I.14, D.33, Y.34, N.35, V.58, D.59, V.60, N.86, A.87, G.88, I.109, A.137, C.138, S.139, Y.152, K.156, P.182, G.183, I.184, V.185, T.187, P.188, M.189, W.190 Ligands: BME.14 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:P.182, D:V.185 Hydrogen bonds: D:G.9, D:G.11, D:Q.12, D:Q.12, D:I.14, D:Y.34, D:D.59, D:V.60, D:N.86, D:Y.152, D:K.156, D:V.185, D:V.185, D:T.187, D:T.187, D:M.189, D:W.190 Water bridges: D:G.15, D:G.15

4 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 7 residues within 4Å: Chain A: S.139, Q.140, Y.152, P.182, G.183, W.190 Ligands: NAD.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.140 BME.6: 7 residues within 4Å: Chain B: S.139, Q.140, Y.152, P.182, G.183, W.190 Ligands: NAD.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.140 BME.10: 7 residues within 4Å: Chain C: S.139, Q.140, Y.152, P.182, G.183, W.190 Ligands: NAD.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.140 BME.14: 7 residues within 4Å: Chain D: S.139, Q.140, Y.152, P.182, G.183, W.190 Ligands: NAD.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.140

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 1 residues within 4Å: Chain C: E.96 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain D: E.96 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otagiri, M. et al., Crystal structure of meso-2,3-butanediol dehydrogenase in a complex with NAD+ and inhibitor mercaptoethanol at 1.7 A resolution for understanding of chiral substrate recognition mechanisms. J.Biochem. (2001)

Release Date

2001-02-28

Peptides

ACETOIN REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

ACETOIN REDUCTASE

Related Entries With Identical Sequence