SMTL ID : 3jv7.1

Structure of ADH-A from Rhodococcus ruber

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.92, A:C.95, A:C.98, A:C.106 ZN.2: 6 residues within 4Å: Chain A: C.38, S.40, H.62, D.153 Ligands: NAD.3, ACY.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.38, A:H.62, A:D.153 ZN.6: 5 residues within 4Å: Chain B: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.92, B:C.95, B:C.98, B:C.106 ZN.7: 6 residues within 4Å: Chain B: C.38, S.40, H.62, D.153 Ligands: NAD.8, ACY.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.38, B:H.62, B:D.153 ZN.11: 5 residues within 4Å: Chain C: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.92, C:C.95, C:C.98, C:C.106 ZN.12: 6 residues within 4Å: Chain C: C.38, S.40, H.62, D.153 Ligands: NAD.13, ACY.14 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.38, C:H.62, C:D.153 ZN.16: 5 residues within 4Å: Chain D: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.92, D:C.95, D:C.98, D:C.106 ZN.17: 6 residues within 4Å: Chain D: C.38, S.40, H.62, D.153 Ligands: NAD.18, ACY.19 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.38, D:H.62, D:D.153

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

NAD.3: 29 residues within 4Å: Chain A: C.38, H.39, S.40, D.153, T.157, I.178, G.179, V.180, G.181, G.182, L.183, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Chain D: F.281 Ligands: ZN.2, ACY.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.157, A:L.183 Hydrogen bonds: A:H.39, A:T.157, A:V.180, A:V.180, A:G.182, A:L.183, A:L.204, A:R.208, A:S.223, A:V.269, A:I.271, A:W.295 Water bridges: A:H.39, A:G.181, A:G.184, A:S.223, A:F.246, A:V.247, A:S.251, A:G.339, A:R.340, A:R.340 Salt bridges: A:H.39, A:R.340 NAD.8: 30 residues within 4Å: Chain B: C.38, H.39, S.40, D.153, T.157, I.178, G.179, V.180, G.181, G.182, L.183, V.202, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Chain C: F.281 Ligands: ZN.7, ACY.9 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.157, B:L.183 Hydrogen bonds: B:H.39, B:V.180, B:V.180, B:G.182, B:L.183, B:L.204, B:S.223, B:S.223, B:I.271, B:P.293, B:W.295 Water bridges: B:H.39, B:G.181, B:G.184, B:R.208, B:R.208, B:G.224, B:V.247, B:S.251, B:I.271, B:R.340, B:R.340 Salt bridges: B:H.39, B:R.340 NAD.13: 28 residues within 4Å: Chain B: F.281 Chain C: C.38, H.39, S.40, D.153, T.157, G.179, V.180, G.181, G.182, L.183, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Ligands: ZN.12, ACY.14 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:T.157, C:L.183 Hydrogen bonds: C:H.39, C:V.180, C:V.180, C:G.182, C:L.183, C:L.204, C:S.223, C:I.271, C:P.293, C:W.295, C:G.339 Water bridges: C:H.39, C:G.181, C:G.184, C:S.223, C:F.246, C:V.247, C:S.251, C:R.340, C:R.340 Salt bridges: C:H.39, C:R.340 NAD.18: 30 residues within 4Å: Chain A: F.281 Chain D: C.38, H.39, S.40, D.153, T.157, I.178, G.179, V.180, G.181, G.182, L.183, V.202, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Ligands: ZN.17, ACY.19 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:T.157, D:L.183 Hydrogen bonds: D:H.39, D:T.157, D:V.180, D:V.180, D:G.182, D:L.183, D:L.204, D:R.208, D:S.223, D:S.223, D:V.269, D:I.271, D:W.295 Water bridges: D:H.39, D:G.181, D:G.184, D:R.208, D:G.224, D:F.246, D:S.251, D:I.271, D:G.339, D:R.340, D:R.340 Salt bridges: D:H.39, D:R.340

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 8 residues within 4Å: Chain A: C.38, S.40, H.62, D.153, W.295 Ligands: ZN.2, NAD.3, MPD.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.295 Hydrogen bonds: A:S.40 Salt bridges: A:H.62 ACY.9: 8 residues within 4Å: Chain B: C.38, S.40, H.62, D.153, W.295 Ligands: ZN.7, NAD.8, MPD.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.295 Hydrogen bonds: B:S.40 Salt bridges: B:H.62 ACY.14: 8 residues within 4Å: Chain C: C.38, S.40, H.62, D.153, W.295 Ligands: ZN.12, NAD.13, MPD.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.295 Hydrogen bonds: C:S.40 Salt bridges: C:H.62 ACY.19: 8 residues within 4Å: Chain D: C.38, S.40, H.62, D.153, W.295 Ligands: ZN.17, NAD.18, MPD.20 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.295 Hydrogen bonds: D:S.40 Salt bridges: D:H.62

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 8 residues within 4Å: Chain A: F.43, V.44, M.47, Y.54, I.271, Y.294 Chain D: F.286 Ligands: ACY.4 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:F.286, A:F.43, A:V.44, A:I.271, A:Y.294 Hydrogen bonds: A:Y.54 Water bridges: A:Y.294 MPD.10: 8 residues within 4Å: Chain B: F.43, V.44, M.47, Y.54, I.271, Y.294 Chain C: F.286 Ligands: ACY.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.43, B:V.44, B:Y.294, C:F.286 MPD.15: 10 residues within 4Å: Chain B: F.282, F.286 Chain C: F.43, V.44, M.47, Y.54, L.119, I.271, Y.294 Ligands: ACY.14 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.43, C:I.271, C:Y.294, B:F.282, B:F.286 Hydrogen bonds: C:Y.54 MPD.20: 7 residues within 4Å: Chain A: F.282, F.286 Chain D: F.43, Y.54, I.271, Y.294 Ligands: ACY.19 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:F.282, A:F.286, D:F.43, D:I.271, D:Y.294 Water bridges: D:Y.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karabec, M. et al., Structural insights into substrate specificity and solvent tolerance in alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541. Chem.Commun.(Camb.) (2010)

Release Date

2010-08-25

Peptides

ADH-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ADH-A

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