SMTL ID : 4i25.1

2.00 Angstroms X-ray crystal structure of NAD- and substrate-bound 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: I.165, S.166, P.167, W.168, N.169, L.174, K.192, P.193, S.194, E.195, F.224, G.225, K.226, G.230, E.231, F.244, T.245, G.246, E.247, T.250, T.253, E.268, L.269, G.270, C.302, E.404, F.406, L.432, F.470, S.476 Ligands: 6OD.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.174, A:T.245 Hydrogen bonds: A:S.166, A:W.168, A:K.192, A:E.195, A:E.247, A:T.250, A:E.404 Water bridges: A:N.169, A:K.226, A:K.226, A:K.226, A:K.226 NAD.6: 30 residues within 4Å: Chain B: I.165, S.166, P.167, W.168, N.169, L.174, K.192, S.194, E.195, F.224, G.225, K.226, G.230, E.231, T.234, F.244, T.245, G.246, E.247, T.250, T.253, E.268, L.269, G.270, C.302, E.404, F.406, L.432, F.470 Ligands: 6OD.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.174, B:T.245 Hydrogen bonds: B:S.166, B:S.166, B:W.168, B:K.192, B:E.195, B:K.226, B:E.247, B:T.250, B:T.250, B:E.268, B:L.269, B:E.404 Water bridges: B:S.248 NAD.7: 30 residues within 4Å: Chain C: I.165, S.166, P.167, W.168, N.169, L.174, K.192, P.193, S.194, E.195, F.224, G.225, K.226, G.230, E.231, F.244, T.245, G.246, E.247, T.250, T.253, E.268, L.269, G.270, C.302, E.404, F.406, L.432, F.470 Ligands: 6OD.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.174, C:T.245 Hydrogen bonds: C:S.166, C:S.166, C:W.168, C:K.192, C:E.195, C:K.226, C:E.247, C:E.247, C:E.268, C:G.271, C:E.404 Water bridges: C:W.168, C:E.231, C:S.248 NAD.10: 29 residues within 4Å: Chain D: I.165, S.166, P.167, W.168, N.169, L.174, K.192, S.194, E.195, F.224, G.225, K.226, G.230, E.231, F.244, T.245, G.246, E.247, T.250, T.253, E.268, L.269, G.270, C.302, E.404, F.406, L.432, F.470 Ligands: 6OD.12 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.174, D:T.245 Hydrogen bonds: D:S.166, D:W.168, D:K.192, D:E.195, D:K.226, D:E.247, D:E.247, D:T.250, D:L.269, D:E.404 Water bridges: D:N.169, D:E.231, D:S.248, D:E.404

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: N.37, I.38, D.105, E.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:I.38 NA.4: 4 residues within 4Å: Chain B: N.37, I.38, D.105, E.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.38, B:E.196 NA.8: 4 residues within 4Å: Chain C: N.37, I.38, D.105, E.196 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.38, C:D.105 NA.11: 4 residues within 4Å: Chain D: N.37, I.38, D.105, E.196 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.37, D:I.38

4 x 6OD: (2E,4E)-2-amino-6-oxohexa-2,4-dienoic acid(Non-covalent)

6OD.3: 11 residues within 4Å: Chain A: R.120, L.173, L.174, W.177, E.268, C.302, L.303, Y.462, R.464, F.470 Ligands: NAD.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.174, A:L.303, A:Y.462, A:F.470 Hydrogen bonds: A:R.120, A:R.120, A:Y.462, A:Y.462, A:R.464 Salt bridges: A:R.120, A:R.464 6OD.5: 10 residues within 4Å: Chain B: R.120, L.173, L.174, W.177, E.268, C.302, Y.462, R.464, F.470 Ligands: NAD.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.174, B:Y.462, B:F.470 Hydrogen bonds: B:R.120, B:R.120, B:Y.462, B:Y.462 Salt bridges: B:R.120, B:R.464 6OD.9: 11 residues within 4Å: Chain C: R.120, L.173, L.174, W.177, E.268, C.302, L.303, Y.462, R.464, F.470 Ligands: NAD.7 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.174, C:Y.462, C:F.470 Hydrogen bonds: C:R.120, C:R.120, C:Y.462, C:R.464 Salt bridges: C:R.120, C:R.464 6OD.12: 10 residues within 4Å: Chain D: R.120, L.173, L.174, W.177, E.268, C.302, Y.462, R.464, F.470 Ligands: NAD.10 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.174, D:Y.462, D:F.470 Hydrogen bonds: D:R.120, D:R.120, D:Y.462, D:R.464 Salt bridges: D:R.120, D:R.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, L. et al., Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action. Nat Commun (2015)

Release Date

2014-05-21

Peptides

2-aminomuconate 6-semialdehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-aminomuconate 6-semialdehyde dehydrogenase

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