SMTL ID : 3meq.1

Crystal structure of alcohol dehydrogenase from Brucella melitensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.63, T.65, H.86, C.173 Ligands: EDO.2, NAI.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.63, A:H.86, A:C.173 ZN.3: 5 residues within 4Å: Chain A: C.117, G.118, C.120, C.123, C.131 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.117, A:C.120, A:C.123, A:C.131 ZN.8: 4 residues within 4Å: Chain B: C.63, H.86, C.173 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.63, B:H.86, B:C.173 ZN.10: 5 residues within 4Å: Chain B: C.117, G.118, C.120, C.123, C.131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.117, B:C.120, B:C.123, B:C.131 ZN.18: 5 residues within 4Å: Chain C: C.63, T.65, H.86, C.173 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.63, C:H.86, C:C.173 ZN.20: 5 residues within 4Å: Chain C: C.117, G.118, C.120, C.123, C.131 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.117, C:C.120, C:C.123, C:C.131 ZN.24: 5 residues within 4Å: Chain D: C.63, T.65, H.86, C.173 Ligands: EDO.25 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.63, D:H.86, D:C.173 ZN.26: 5 residues within 4Å: Chain D: C.117, G.118, C.120, C.123, C.131 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.117, D:C.120, D:C.123, D:C.131

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: C.63, T.65, W.74, H.86, W.112, C.173, L.289 Ligands: ZN.1, NAI.4 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: D.324, F.325, D.328, K.330 Chain C: G.190, N.215 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: V.76, W.112, Y.139 Chain D: L.303 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain B: C.63, T.65, H.86, W.112, C.173, L.289, I.312, V.313 Ligands: ZN.8 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: P.111, W.112, L.113, G.314, T.315, R.316, L.319 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain B: T.129, L.130, G.310, S.311, I.312, V.313 Chain C: V.302, L.303, G.305 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: V.62, H.64, M.350, G.357, R.358, I.359 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: L.182, K.183, T.187, M.212, L.214 Chain D: P.189 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: I.45, Q.47, Q.54, S.93, Y.148 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: G.190, N.215 Chain D: D.324, F.325, D.328, K.330 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: R.107, K.161, N.162, I.163, D.164 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain C: C.63, T.65, H.86, W.112, C.173, L.289, V.313 Ligands: ZN.18 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: G.190, N.215 Chain C: D.324, F.325, D.328 Ligand excluded by PLIP EDO.25: 9 residues within 4Å: Chain D: C.63, T.65, H.86, W.112, C.173, L.289, I.312, V.313 Ligands: ZN.24 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain D: L.275, N.300, M.301, N.304 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain D: V.62, H.64, M.350, G.357, R.358, I.359 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain A: V.302, L.303, G.305 Chain D: T.129, L.130, S.311, I.312, V.313 Ligand excluded by PLIP

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.4: 33 residues within 4Å: Chain A: C.63, H.64, T.65, H.68, W.74, C.173, T.177, S.196, G.197, I.198, G.199, G.200, L.201, D.220, I.221, K.225, T.264, A.265, V.266, S.267, A.270, N.287, G.288, L.289, P.290, S.311, I.312, V.313, M.350, R.358 Chain D: V.302 Ligands: ZN.1, EDO.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.177, A:L.201 Hydrogen bonds: A:H.64, A:T.65, A:H.68, A:I.198, A:I.198, A:G.200, A:L.201, A:V.266, A:S.267, A:S.267, A:N.287, A:N.287, A:L.289, A:V.313 Water bridges: A:G.199, A:G.202, A:G.357, A:R.358 Salt bridges: A:H.64, A:R.358

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: R.210 Chain C: R.210, A.211 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain C: L.228, R.231 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.23: 4 residues within 4Å: Chain C: Y.114, N.142, V.149, V.150 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.114, C:Y.114, C:V.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arakaki, T.L. et al., Crystal structure of alcohol dehydrogenase from Brucella melitensis. To be Published

Release Date

2010-04-28

Peptides

Alcohol dehydrogenase, zinc-containing: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alcohol dehydrogenase, zinc-containing