SMTL ID : 6n7l.1 (2 other biounits)

Crystal structure of an alcohol dehydrogenase from Elizabethkingia anophelis NUHP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: D.309, F.310, E.313, L.315 Chain C: G.177, H.202 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: K.170, E.171, E.173 Chain D: R.290 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: A.64, Y.126 Chain D: L.288 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: G.105, C.110, R.301 Chain B: G.105, C.110, R.301 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: P.253, I.254, K.257, F.279, E.280 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.208, A.227, I.254, Q.258 Ligands: NAD.2 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: V.18, V.31, K.67, P.69, L.70, I.71, D.129 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Y.142, R.301 Chain B: G.105, C.106 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: C.106, C.107, D.108, I.111 Chain B: R.301, K.302, Q.305 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: T.224, T.230, Y.235 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: K.197, A.198 Chain C: K.197, A.198, G.200 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: D.309, F.310, E.313, L.315 Chain D: G.177, H.202 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: A.64, N.123, Y.126 Chain C: L.288 Ligands: EDO.34 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: P.253, I.254, K.257, F.279, E.280 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: M.14, R.34, D.129 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: K.197, A.198, G.200 Chain D: K.197, A.198, G.200 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: V.208, A.227, I.254, Q.258 Ligands: NAD.17 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: V.18, V.31, K.67, P.69, I.71, D.129 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: G.177, H.202 Chain C: D.309, F.310, E.313, L.315 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: L.288 Chain C: A.64, N.123, Y.126 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: M.14, V.31, R.34, D.129 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: T.224, T.230, Y.235 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: Y.109, E.119 Chain C: H.237, L.263, R.264, R.265, K.289 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: C.104, A.120 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: R.265, F.284, K.289 Ligands: EDO.18 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain C: M.46, D.347, A.349, G.350 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: V.18, K.67, P.69, D.129 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: R.290 Chain C: K.170, E.171, E.173, R.294 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain C: K.217, A.221, D.222, L.223, T.224 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: A.227, I.254, Q.258 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain A: L.288 Chain D: A.64, N.123, Y.126 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain C: G.105, C.110, R.301 Chain D: G.105, C.110, R.301 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain B: G.177, H.202 Chain D: D.309, F.310, E.313, L.315 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain D: V.31, K.67, P.69, I.71, D.129 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain D: M.14, V.31, R.34, I.71, D.129 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: M.46, D.347, G.350 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain A: R.290 Chain D: K.170, E.171, R.294 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: D.211, E.214, L.215, K.218, D.341 Ligand excluded by PLIP

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

NAD.2: 34 residues within 4Å: Chain A: C.51, H.52, T.53, H.56, W.62, C.160, T.164, S.183, G.184, I.185, G.186, G.187, L.188, I.206, D.207, V.208, K.212, T.249, A.250, V.251, S.252, I.254, A.255, N.272, G.273, L.274, S.296, I.297, V.298, M.335, R.343 Chain D: V.287 Ligands: EDO.7, ZN.13 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.164, A:L.188 Hydrogen bonds: A:H.52, A:H.56, A:I.185, A:I.185, A:G.187, A:L.188, A:V.251, A:N.272, A:N.272, A:L.274, A:V.298 Water bridges: A:S.183, A:S.183, A:G.186, A:G.189, A:S.252, A:S.252, A:R.343 Salt bridges: A:H.52, A:H.52, A:R.343 NAD.17: 34 residues within 4Å: Chain B: C.51, H.52, T.53, H.56, W.62, C.160, T.164, S.183, G.184, I.185, G.186, G.187, L.188, I.206, D.207, V.208, K.212, T.249, A.250, V.251, I.254, A.255, N.272, G.273, L.274, P.275, S.296, I.297, V.298, M.335, R.343 Chain C: V.287 Ligands: EDO.22, ZN.24 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.164, B:L.188 Hydrogen bonds: B:H.52, B:T.53, B:H.56, B:T.164, B:I.185, B:I.185, B:G.187, B:L.188, B:N.272, B:N.272, B:L.274, B:V.298 Water bridges: B:G.186, B:G.189, B:S.252, B:S.252, B:Q.258, B:R.343 Salt bridges: B:H.52, B:R.343 NAD.28: 33 residues within 4Å: Chain B: V.287 Chain C: C.51, H.52, T.53, H.56, W.62, C.160, T.164, S.183, G.184, I.185, G.186, G.187, L.188, I.206, D.207, V.208, K.212, T.249, A.250, V.251, S.252, I.254, A.255, N.272, G.273, L.274, S.296, I.297, V.298, M.335, R.343 Ligands: ZN.40 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:T.164, C:L.188 Hydrogen bonds: C:H.52, C:T.53, C:H.56, C:I.185, C:I.185, C:G.187, C:L.188, C:V.251, C:S.252, C:S.252, C:N.272, C:N.272, C:L.274, C:V.298 Water bridges: C:G.186, C:G.189, C:R.343 Salt bridges: C:H.52, C:R.343 NAD.43: 33 residues within 4Å: Chain A: V.287 Chain D: C.51, H.52, T.53, H.56, W.62, C.160, T.164, S.183, G.184, I.185, G.186, G.187, L.188, I.206, D.207, V.208, K.212, T.249, A.250, V.251, S.252, I.254, A.255, N.272, G.273, L.274, S.296, I.297, V.298, M.335, R.343 Ligands: ZN.52 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:T.164, D:L.188 Hydrogen bonds: D:H.52, D:H.56, D:I.185, D:I.185, D:G.187, D:L.188, D:V.251, D:S.252, D:N.272, D:N.272, D:L.274, D:V.298 Water bridges: D:S.183, D:S.183, D:G.186, D:G.189, D:S.252, D:R.343 Salt bridges: D:H.52, D:R.343

8 x ZN: ZINC ION(Non-covalent)

ZN.13: 5 residues within 4Å: Chain A: C.51, T.53, H.74, C.160 Ligands: NAD.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.51, A:H.74, A:C.160, H2O.3 ZN.14: 5 residues within 4Å: Chain A: C.104, G.105, C.107, C.110, C.118 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.104, A:C.107, A:C.110, A:C.118 ZN.24: 5 residues within 4Å: Chain B: C.51, T.53, H.74, C.160 Ligands: NAD.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.51, B:H.74, B:C.160, H2O.15 ZN.25: 5 residues within 4Å: Chain B: C.104, G.105, C.107, C.110, C.118 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.104, B:C.107, B:C.110, B:C.118 ZN.40: 5 residues within 4Å: Chain C: C.51, T.53, H.74, C.160 Ligands: NAD.28 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.51, C:H.74, C:C.160, H2O.23 ZN.41: 5 residues within 4Å: Chain C: C.104, G.105, C.107, C.110, C.118 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.104, C:C.107, C:C.110, C:C.118 ZN.52: 5 residues within 4Å: Chain D: C.51, T.53, H.74, C.160 Ligands: NAD.43 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.51, D:H.74, D:C.160, H2O.32 ZN.53: 5 residues within 4Å: Chain D: C.104, G.105, C.107, C.110, C.118 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.104, D:C.107, D:C.110, D:C.118

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

CL.15: 3 residues within 4Å: Chain A: L.146, K.147, V.150 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: L.146, K.147, V.150 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain C: L.146, K.147, V.150 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain D: L.146, K.147, V.150 Ligand excluded by PLIP

Links

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Citation

Edwards, T.E. et al., Crystal structure of an alcohol dehydrogenase from Elizabethkingia anophelis NUHP1. To Be Published

Release Date

2018-12-12

Peptides

Alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alcohol dehydrogenase

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