SMTL ID : 5ej2.1 (1 other biounit)

Crystal structure of Carveol dehydrogenase from Mycobacterium avium in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: G.44, A.46, R.47, G.48, Q.49, D.68, I.69, I.73, Y.78, S.81, V.105, D.106, V.107, R.108, N.133, A.134, G.135, V.136, I.157, T.185, S.186, S.187, Y.200, K.204, P.230, T.231, Q.232, V.233, T.235, M.237, V.238 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.49, A:Q.49, A:I.69, A:S.81, A:S.81, A:D.106, A:V.107, A:N.133, A:G.135, A:K.204, A:V.233, A:V.233, A:T.235, A:T.236 Water bridges: A:G.50, A:S.81, A:N.133 Salt bridges: A:R.47 NAD.4: 31 residues within 4Å: Chain B: G.44, A.46, R.47, G.48, Q.49, D.68, I.69, I.73, Y.78, S.81, V.105, D.106, V.107, R.108, N.133, A.134, G.135, V.136, I.157, T.185, S.186, S.187, Y.200, K.204, P.230, T.231, Q.232, V.233, T.235, M.237, V.238 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.49, B:Q.49, B:I.69, B:S.81, B:S.81, B:D.106, B:V.107, B:N.133, B:G.135, B:Y.200, B:K.204, B:V.233, B:V.233, B:T.235, B:T.235 Water bridges: B:G.50, B:Y.78, B:S.81, B:N.133 Salt bridges: B:R.47 NAD.6: 31 residues within 4Å: Chain C: G.44, A.46, R.47, G.48, Q.49, D.68, I.69, I.73, Y.78, S.81, V.105, D.106, V.107, R.108, N.133, A.134, G.135, V.136, I.157, T.185, S.186, S.187, Y.200, K.204, P.230, T.231, Q.232, V.233, T.235, M.237, V.238 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:Q.49, C:Q.49, C:I.69, C:S.81, C:S.81, C:D.106, C:D.106, C:V.107, C:N.133, C:G.135, C:Y.200, C:K.204, C:V.233, C:V.233, C:T.235, C:T.235, C:T.236 Water bridges: C:G.50, C:Y.78, C:S.81, C:N.133 Salt bridges: C:R.47 NAD.9: 31 residues within 4Å: Chain D: G.44, A.46, R.47, G.48, Q.49, D.68, I.69, I.73, Y.78, S.81, V.105, D.106, V.107, R.108, N.133, A.134, G.135, V.136, I.157, T.185, S.186, S.187, Y.200, K.204, P.230, T.231, Q.232, V.233, T.235, M.237, V.238 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.49, D:Q.49, D:I.69, D:S.81, D:S.81, D:D.106, D:V.107, D:N.133, D:G.135, D:K.204, D:V.233, D:V.233, D:T.235 Water bridges: D:G.50, D:S.81, D:N.133 Salt bridges: D:R.47

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.191, R.212 Chain B: R.191, R.212 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:S.298 Salt bridges: B:R.191, B:R.212, A:R.191, A:R.212 PO4.7: 4 residues within 4Å: Chain C: R.191, R.212 Chain D: R.191, R.212 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Salt bridges: C:R.191, C:R.212, D:R.191, D:R.212 Water bridges: D:S.298

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

MPD.3: 4 residues within 4Å: Chain A: Y.194, P.195, T.197, F.247 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.194, A:T.197, A:F.247, A:F.247 Hydrogen bonds: A:P.195 MPD.5: 5 residues within 4Å: Chain B: Y.194, P.195, T.197, L.246, F.247 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.197, B:F.247, B:F.247 Hydrogen bonds: B:P.195 MPD.8: 4 residues within 4Å: Chain C: Y.194, P.195, T.197, F.247 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.194, C:T.197, C:F.247, C:F.247 Hydrogen bonds: C:P.195 MPD.10: 5 residues within 4Å: Chain D: Y.194, P.195, T.197, L.246, F.247 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.197, D:F.247, D:F.247 Hydrogen bonds: D:P.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haft, D.H. et al., Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep (2017)

Release Date

2015-12-02

Peptides

Carveol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Carveol dehydrogenase

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