SMTL ID : 3a28.1 (1 other biounit)

Crystal structure of L-2,3-butanediol dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.9, Q.12, G.13, I.14, D.33, L.34, Q.37, L.60, D.61, V.62, T.63, N.88, A.89, G.90, V.111, A.139, A.140, S.141, Y.154, K.158, P.184, G.185, I.186, V.187, T.189, M.191, W.192 Ligands: BME.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.184 Hydrogen bonds: A:Q.12, A:Q.12, A:Q.12, A:I.14, A:L.34, A:Q.37, A:D.61, A:D.61, A:V.62, A:N.88, A:G.90, A:Y.154, A:K.158, A:V.187, A:V.187, A:T.189, A:G.190 Water bridges: A:G.15, A:N.88, A:N.88 NAD.4: 30 residues within 4Å: Chain B: G.9, A.11, Q.12, G.13, I.14, D.33, L.34, Q.37, L.60, D.61, V.62, T.63, N.88, A.89, G.90, V.111, A.139, A.140, S.141, Y.154, K.158, P.184, G.185, I.186, V.187, T.189, G.190, M.191, W.192 Ligands: BME.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.184 Hydrogen bonds: B:G.9, B:Q.12, B:Q.12, B:I.14, B:L.34, B:Q.37, B:D.61, B:D.61, B:V.62, B:N.88, B:G.90, B:Y.154, B:K.158, B:V.187, B:V.187, B:T.189, B:T.189, B:G.190, B:M.191 Water bridges: B:G.13, B:G.15, B:G.15 NAD.7: 30 residues within 4Å: Chain C: G.9, Q.12, G.13, I.14, D.33, L.34, Q.37, L.60, D.61, V.62, T.63, N.88, A.89, G.90, I.91, V.111, A.139, A.140, S.141, Y.154, K.158, P.184, G.185, I.186, V.187, T.189, G.190, M.191, W.192 Ligands: BME.8 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.184 Hydrogen bonds: C:G.9, C:Q.12, C:Q.12, C:I.14, C:G.15, C:L.34, C:Q.37, C:D.61, C:V.62, C:N.88, C:G.90, C:K.158, C:V.187, C:V.187, C:T.189, C:G.190, C:M.191 Water bridges: C:N.88 NAD.9: 31 residues within 4Å: Chain D: G.9, A.11, Q.12, G.13, I.14, D.33, L.34, Q.37, L.60, D.61, V.62, T.63, N.88, A.89, G.90, I.91, V.111, A.139, A.140, S.141, Y.154, K.158, P.184, G.185, I.186, V.187, T.189, G.190, M.191, W.192 Ligands: BME.10 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:P.184 Hydrogen bonds: D:Q.12, D:Q.12, D:Q.12, D:I.14, D:L.34, D:Q.37, D:D.61, D:V.62, D:N.88, D:G.90, D:Y.154, D:K.158, D:V.187, D:V.187, D:T.189, D:T.189, D:G.190, D:M.191 Water bridges: D:G.15, D:G.15

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

BME.2: 6 residues within 4Å: Chain A: S.141, Y.154, G.185, I.186, W.192 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) BME.5: 7 residues within 4Å: Chain B: S.141, I.142, Y.154, G.185, I.186, W.192 Ligands: NAD.4 No protein-ligand interaction detected (PLIP) BME.8: 7 residues within 4Å: Chain C: S.141, I.142, Y.154, G.185, I.186, W.192 Ligands: NAD.7 No protein-ligand interaction detected (PLIP) BME.10: 7 residues within 4Å: Chain D: S.141, I.142, Y.154, G.185, I.186, W.192 Ligands: NAD.9 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: F.235, N.240 Chain D: F.235 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: F.235 Chain C: F.235 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otagiri, M. et al., Structural basis for chiral substrate recognition by two 2,3-butanediol dehydrogenases. Febs Lett. (2010)

Release Date

2009-12-15

Peptides

L-2.3-butanediol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

L-2.3-butanediol dehydrogenase

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