SMTL ID : 3s2e.1 (1 other biounit)

Crystal Structure of FurX NADH Complex 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.40, H.63, E.64, C.150 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.40, A:H.63, A:E.64, A:C.150 ZN.2: 5 residues within 4Å: Chain A: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.94, A:C.97, A:C.100, A:C.108 ZN.8: 4 residues within 4Å: Chain B: C.40, H.63, E.64, C.150 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.40, B:H.63, B:E.64, B:C.150 ZN.9: 5 residues within 4Å: Chain B: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.94, B:C.97, B:C.100, B:C.108 ZN.15: 5 residues within 4Å: Chain C: C.40, T.42, H.63, C.150 Ligands: NAD.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.40, C:H.63, C:C.150, H2O.33 ZN.16: 5 residues within 4Å: Chain C: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.94, C:C.97, C:C.100, C:C.108 ZN.18: 5 residues within 4Å: Chain D: C.40, T.42, H.63, C.150 Ligands: NAD.17 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.40, D:H.63, D:C.150, H2O.44 ZN.19: 5 residues within 4Å: Chain D: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.94, D:C.97, D:C.100, D:C.108

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.42, H.63, W.89, C.150, I.287, V.288 5 PLIP interactions: 5 interactions with chain A Water bridges: A:T.42, A:T.42, A:T.42, A:H.63, A:W.89 GOL.4: 7 residues within 4Å: Chain A: H.41, T.42, H.45, W.51, G.263, L.264, I.287 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.42, A:H.45, A:L.264 Water bridges: A:T.42, A:T.42, A:N.262 GOL.5: 7 residues within 4Å: Chain A: W.51, P.52, V.53, W.89, Y.116 Chain D: F.274, L.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.53 Water bridges: A:W.89 GOL.10: 6 residues within 4Å: Chain B: T.42, H.63, W.89, C.150, I.287, V.288 6 PLIP interactions: 6 interactions with chain B Water bridges: B:T.42, B:T.42, B:T.42, B:H.63, B:W.89, B:T.154 GOL.11: 7 residues within 4Å: Chain B: W.51, P.52, V.53, W.89, Y.116 Chain C: F.274, L.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.53 Water bridges: B:W.89

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: C.40, H.41, G.177, R.333 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.41 Water bridges: A:T.42, A:G.177, A:G.177, A:G.177, A:G.177, A:L.178 Salt bridges: A:H.41, A:R.333 SO4.7: 3 residues within 4Å: Chain A: R.84, G.141, F.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.142 Salt bridges: A:R.84 SO4.12: 4 residues within 4Å: Chain B: C.40, H.41, G.177, R.333 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.41 Water bridges: B:T.42, B:G.177, B:L.178 Salt bridges: B:H.41, B:R.333 SO4.13: 3 residues within 4Å: Chain B: R.84, G.141, F.142 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.142 Water bridges: B:Y.68, B:R.84, B:R.84, B:V.143 Salt bridges: B:R.84 SO4.20: 3 residues within 4Å: Chain D: R.84, G.141, F.142 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.142 Water bridges: D:E.35, D:V.143 Salt bridges: D:R.84 SO4.21: 2 residues within 4Å: Chain D: N.204, R.208 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.208, D:R.208 Salt bridges: D:R.208

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

NAD.14: 30 residues within 4Å: Chain B: V.277 Chain C: C.40, H.41, T.42, C.150, T.154, S.173, G.174, I.175, G.176, G.177, L.178, V.196, D.197, I.198, K.202, T.239, A.240, V.241, S.242, A.245, N.262, G.263, L.264, S.286, I.287, V.288, L.325, R.333 Ligands: ZN.15 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:T.154 Hydrogen bonds: C:H.41, C:T.154, C:I.175, C:G.177, C:L.178, C:D.197, C:V.241, C:S.242, C:S.242, C:N.262, C:L.264, C:V.288 Water bridges: C:H.41, C:G.176, C:G.179, C:R.218, C:K.244, C:R.333, C:R.333 Salt bridges: C:H.41, C:R.333 NAD.17: 30 residues within 4Å: Chain A: V.277 Chain D: C.40, H.41, T.42, H.45, C.150, T.154, S.173, G.174, I.175, G.176, G.177, L.178, D.197, I.198, K.202, T.239, A.240, V.241, S.242, A.245, N.262, G.263, L.264, S.286, I.287, V.288, L.325, R.333 Ligands: ZN.18 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:T.154, D:L.178 Hydrogen bonds: D:H.41, D:H.45, D:T.154, D:I.175, D:I.175, D:G.177, D:L.178, D:V.241, D:S.242, D:S.242, D:N.262, D:L.264, D:V.288 Water bridges: D:G.176, D:G.179, D:R.218, D:R.218, D:R.218, D:R.218, D:R.333 Salt bridges: D:H.41, D:R.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayes, R. et al., Crystal Structures and furfural reduction mechanism of a bacterial zinc-dependent alcohol dehydrogenase. To be Published

Release Date

2012-06-13

Peptides

Zinc-containing alcohol dehydrogenase superfamily: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
F

D
G

Zinc-containing alcohol dehydrogenase superfamily

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