SMTL ID : 5xtg.1

Crystal structure of the cis-dihydrodiol naphthalene dehydrogenase NahB from Pseudomonas sp. MC1 in the presence of NAD+ and 2,3-dihydroxybiphenyl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 33 residues within 4Å: Chain A: G.30, G.32, S.33, G.34, I.35, G.36, L.53, R.55, Q.59, G.76, D.77, V.78, R.79, N.104, A.105, G.106, I.107, I.131, Y.136, T.157, A.158, S.159, V.160, S.161, Y.172, K.176, P.201, G.202, G.203, T.204, T.206, S.207 Ligands: BPY.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.32, A:S.33, A:S.33, A:S.33, A:S.33, A:I.35, A:Q.59, A:D.77, A:V.78, A:R.79, A:R.79, A:A.105, A:G.106, A:K.176, A:G.203, A:T.204, A:T.204, A:T.206 Water bridges: A:R.55 NAD.4: 33 residues within 4Å: Chain B: G.30, G.32, S.33, G.34, I.35, G.36, L.53, R.55, Q.59, G.76, D.77, V.78, R.79, N.104, A.105, G.106, I.107, I.131, Y.136, T.157, A.158, S.159, V.160, S.161, Y.172, K.176, P.201, G.202, G.203, T.204, T.206, S.207 Ligands: BPY.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.32, B:S.33, B:S.33, B:S.33, B:S.33, B:I.35, B:Q.59, B:D.77, B:V.78, B:R.79, B:R.79, B:A.105, B:G.106, B:K.176, B:G.203, B:T.204, B:T.204, B:T.206 Water bridges: B:R.55 NAD.7: 33 residues within 4Å: Chain C: G.30, G.32, S.33, G.34, I.35, G.36, L.53, R.55, Q.59, G.76, D.77, V.78, R.79, N.104, A.105, G.106, I.107, I.131, Y.136, T.157, A.158, S.159, V.160, S.161, Y.172, K.176, P.201, G.202, G.203, T.204, T.206, S.207 Ligands: BPY.9 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.32, C:S.33, C:S.33, C:S.33, C:S.33, C:I.35, C:Q.59, C:D.77, C:V.78, C:R.79, C:R.79, C:A.105, C:G.106, C:K.176, C:G.203, C:T.204, C:T.204, C:T.206 Water bridges: C:R.55 NAD.10: 33 residues within 4Å: Chain D: G.30, G.32, S.33, G.34, I.35, G.36, L.53, R.55, Q.59, G.76, D.77, V.78, R.79, N.104, A.105, G.106, I.107, I.131, Y.136, T.157, A.158, S.159, V.160, S.161, Y.172, K.176, P.201, G.202, G.203, T.204, T.206, S.207 Ligands: BPY.12 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:G.32, D:S.33, D:S.33, D:S.33, D:S.33, D:I.35, D:Q.59, D:D.77, D:V.78, D:R.79, D:R.79, D:A.105, D:G.106, D:K.176, D:G.203, D:T.204, D:T.204, D:T.206 Water bridges: D:R.55

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 8 residues within 4Å: Chain A: E.60, C.64, K.68, D.69, L.71, E.72, I.73, R.94 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.73 Hydrogen bonds: A:I.73 CIT.5: 8 residues within 4Å: Chain B: E.60, C.64, K.68, D.69, L.71, E.72, I.73, R.94 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.73 Hydrogen bonds: B:I.73 CIT.8: 8 residues within 4Å: Chain C: E.60, C.64, K.68, D.69, L.71, E.72, I.73, R.94 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.73 Hydrogen bonds: C:E.60, C:I.73 CIT.11: 8 residues within 4Å: Chain D: E.60, C.64, K.68, D.69, L.71, E.72, I.73, R.94 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.73 Hydrogen bonds: D:E.60, D:I.73

4 x BPY: BIPHENYL-2,3-DIOL(Non-covalent)

BPY.3: 5 residues within 4Å: Chain A: W.108, Y.172, T.206, S.207 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) BPY.6: 5 residues within 4Å: Chain B: W.108, Y.172, T.206, S.207 Ligands: NAD.4 No protein-ligand interaction detected (PLIP) BPY.9: 5 residues within 4Å: Chain C: W.108, Y.172, T.206, S.207 Ligands: NAD.7 No protein-ligand interaction detected (PLIP) BPY.12: 5 residues within 4Å: Chain D: W.108, Y.172, T.206, S.207 Ligands: NAD.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, A.K. et al., Crystal structure of cis-dihydrodiol naphthalene dehydrogenase (NahB) from Pseudomonas sp. MC1: Insights into the early binding process of the substrate. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-08-09

Peptides

2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase

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