SMTL ID : 4oe2.1

2.00 Angstroms X-ray crystal structure of E268A 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 32 residues within 4Å: Chain A: 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, T.217, F.227, T.228, G.229, E.230, T.233, T.236, I.237, A.251, L.252, G.253, C.285, E.387, F.389, L.415, F.453 Ligands: GOL.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.157, A:T.228 Hydrogen bonds: A:W.151, A:K.175, A:K.175, A:E.178, A:E.230, A:E.230, A:E.387 Water bridges: A:E.178, A:G.208, A:K.209, A:T.217 NAD.4: 31 residues within 4Å: Chain B: 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, 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: GOL.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:P.176, B:E.178, B:K.209, B:E.230, B:E.230, B:T.233, B:E.387, B:E.387 Water bridges: B:E.214, B:T.217, B:T.228, B:S.231 NAD.7: 32 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, T.217, F.227, T.228, G.229, E.230, T.233, T.236, I.237, A.251, L.252, G.253, C.285, E.387, F.389, L.415, F.453 Ligands: GOL.9 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.157, C:T.228 Hydrogen bonds: C:S.149, C:W.151, C:K.175, C:K.175, C:K.209, C:E.230, C:T.233, C:E.387 Water bridges: C:S.231, C:E.387 NAD.10: 31 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, 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: GOL.12 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.157, D:T.228 Hydrogen bonds: D:W.151, D:K.175, D:P.176, D:E.178, D:K.209, D:E.230, D:T.233, D:T.233, D:L.252, D:E.387 Water bridges: D:E.214, D:E.387

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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: R.103, L.156, L.157, W.160, Y.445, R.447, F.453 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:R.103, A:Y.445, A:R.447 Water bridges: A:W.160 GOL.6: 7 residues within 4Å: Chain B: R.103, L.157, W.160, Y.445, R.447, F.453 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.103, B:R.103, B:Y.445, B:R.447, B:R.447 Water bridges: B:W.160 GOL.9: 7 residues within 4Å: Chain C: R.103, L.157, W.160, Y.445, R.447, F.453 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.103, C:R.103, C:Y.445, C:Y.445, C:R.447 Water bridges: C:W.160, C:W.160 GOL.12: 8 residues within 4Å: Chain D: R.103, L.156, L.157, W.160, Y.445, R.447, F.453 Ligands: NAD.10 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.103, D:R.103, D:Y.445, D:Y.445, D:R.447 Water bridges: D:W.160

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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