SMTL ID : 4ou2.1

A 2.15 Angstroms X-ray crystal structure of E268A 2-aminomuconate 6-semialdehyde dehydrogenase catalytic intermediate from Pseudomonas fluorescens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: I.148, S.149, P.150, W.151, N.152, L.157, K.175, S.177, E.178, F.207, G.208, K.209, G.213, E.214, T.217, F.227, T.228, G.229, E.230, T.233, T.236, A.251, L.252, G.253, C.285, E.387, F.389, L.415, F.453 Ligands: 6OA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.150, A:L.157, A:T.228 Hydrogen bonds: A:S.149, A:W.151, A:K.175, A:E.178, A:E.230, A:E.230, A:T.233, A:L.252, A:E.387 Water bridges: A:G.208, A:S.231 NAD.4: 29 residues within 4Å: Chain B: I.148, S.149, P.150, W.151, N.152, L.157, K.175, S.177, E.178, F.207, G.208, K.209, G.213, E.214, F.227, T.228, G.229, E.230, T.233, T.236, A.251, L.252, G.253, C.285, E.387, F.389, L.415, F.453 Ligands: 6OA.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.157, B:T.228 Hydrogen bonds: B:S.149, B:W.151, B:K.175, B:E.178, B:E.230, B:E.230, B:T.233, B:T.233, B:L.252, B:E.387 Water bridges: B:K.209, B:K.209, B:T.228, B:S.231, B:E.387 NAD.7: 30 residues within 4Å: Chain C: I.148, S.149, P.150, W.151, N.152, L.157, K.175, P.176, S.177, E.178, F.207, G.208, K.209, G.213, E.214, F.227, T.228, G.229, E.230, T.233, T.236, A.251, L.252, G.253, C.285, E.387, F.389, L.415, F.453 Ligands: 6OA.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.157, C:T.228 Hydrogen bonds: C:S.149, C:S.149, C:W.151, C:K.175, C:E.178, C:K.209, C:E.230, C:E.230, C:T.233, C:L.252, C:G.254, C:E.387 Water bridges: C:G.208, C:S.231 NAD.10: 30 residues within 4Å: Chain D: I.148, S.149, P.150, W.151, N.152, L.157, K.175, P.176, S.177, E.178, F.207, G.208, K.209, G.213, E.214, F.227, T.228, G.229, E.230, T.233, T.236, A.251, L.252, G.253, C.285, E.387, F.389, L.415, F.453 Ligands: 6OA.12 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:P.150, D:L.157, D:T.228 Hydrogen bonds: D:S.149, D:W.151, D:K.175, D:E.178, D:K.209, D:E.230, D:E.230, D:T.233, D:L.252, D:E.387 Water bridges: D:T.217, D:S.231

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

NA.2: 4 residues within 4Å: Chain A: N.20, I.21, D.88, E.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.21, A:D.88 NA.5: 4 residues within 4Å: Chain B: N.20, I.21, D.88, E.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.21, B:E.179 NA.8: 5 residues within 4Å: Chain C: N.20, I.21, D.88, E.179, I.328 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.21, C:E.179 NA.11: 3 residues within 4Å: Chain D: N.20, I.21, E.179 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.21, D:E.179, D:E.179

4 x 6OA: (2Z,4E)-2,6-dihydroxyhexa-2,4-dienoic acid(Covalent)

6OA.3: 12 residues within 4Å: Chain A: R.103, N.152, L.153, L.156, L.157, W.160, V.284, C.285, Y.445, R.447, F.453 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.153, A:L.157, A:Y.445, A:F.453 Hydrogen bonds: A:N.152, A:C.285, A:Y.445, A:Y.445 Salt bridges: A:R.103, A:R.447 6OA.6: 12 residues within 4Å: Chain B: R.103, N.152, L.156, L.157, W.160, V.284, C.285, L.286, Y.445, R.447, F.453 Ligands: NAD.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.157, B:L.286, B:F.453 Hydrogen bonds: B:N.152, B:W.160, B:C.285, B:Y.445 Water bridges: B:W.160, B:K.161 Salt bridges: B:R.103, B:R.447 6OA.9: 12 residues within 4Å: Chain C: R.103, N.152, L.156, L.157, W.160, V.284, C.285, L.286, Y.445, R.447, F.453 Ligands: NAD.7 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.157, C:V.284, C:L.286, C:F.453 Hydrogen bonds: C:N.152, C:C.285, C:Y.445 Water bridges: C:W.160 Salt bridges: C:R.103, C:R.447 6OA.12: 12 residues within 4Å: Chain D: R.103, N.152, L.156, L.157, W.160, V.284, C.285, L.286, Y.445, R.447, F.453 Ligands: NAD.10 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.157, D:L.286, D:F.453 Hydrogen bonds: D:N.152, D:W.160, D:C.285 Water bridges: D:W.160 Salt bridges: D:R.103, D:R.447

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

2014-12-24

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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