SMTL ID : 4npi.1

1.94 Angstroms X-ray crystal structure of NAD- and intermediate- bound alpha-aminomuconate-epsilon-semialdehyde dehydrogenase from Pseudomonas fluorescens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: I.148, S.149, P.150, W.151, N.152, 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, E.251, L.252, G.253, C.285, H.332, K.335, E.387, F.389 Ligands: 2VS.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.150 Hydrogen bonds: A:S.149, A:N.152, A:K.175, A:E.178, A:G.229, A:E.230, A:E.251, A:K.335, A:K.335 Water bridges: A:E.178, A:E.178, A:G.208, A:E.214, A:H.332 pi-Stacking: A:F.389 NAD.4: 28 residues within 4Å: Chain B: I.148, S.149, P.150, W.151, N.152, 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, E.251, L.252, G.253, C.285, H.332, K.335, E.387, F.389 Ligands: 2VS.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.150 Hydrogen bonds: B:S.149, B:S.149, B:N.152, B:K.175, B:E.178, B:K.209, B:E.230, B:T.233, B:E.251, B:H.332, B:K.335, B:K.335 Water bridges: B:G.208, B:G.208, B:E.214, B:E.214, B:T.217 pi-Stacking: B:F.389 NAD.7: 28 residues within 4Å: Chain C: I.148, S.149, P.150, W.151, N.152, 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, E.251, L.252, G.253, C.285, K.335, E.387, F.389 Ligands: 2VS.9 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.150 Hydrogen bonds: C:S.149, C:N.152, C:K.175, C:E.178, C:K.209, C:G.229, C:E.230, C:E.230, C:T.233, C:T.233, C:E.251, C:K.335, C:K.335, C:E.387 Water bridges: C:E.230, C:H.332, C:K.335 pi-Stacking: C:F.389 NAD.10: 28 residues within 4Å: Chain D: I.148, S.149, P.150, W.151, N.152, 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, E.251, L.252, G.253, C.285, H.332, K.335, E.387, F.389 Ligands: 2VS.12 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.150 Hydrogen bonds: D:S.149, D:S.149, D:N.152, D:K.175, D:E.178, D:K.209, D:G.229, D:E.230, D:T.233, D:T.233, D:E.251, D:H.332, D:K.335, D:K.335, D:E.387 Water bridges: D:E.178, D:E.178 pi-Stacking: D:F.389

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:D.88 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 2VS: (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid(Covalent)

2VS.3: 13 residues within 4Å: Chain A: R.103, N.152, L.153, L.156, L.157, W.160, E.251, 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:F.453 Hydrogen bonds: A:N.152, A:W.160, A:C.285 Water bridges: A:E.251, A:E.251 Salt bridges: A:R.103, A:R.447 2VS.6: 12 residues within 4Å: Chain B: R.103, N.152, L.153, L.157, W.160, E.251, V.284, C.285, Y.445, R.447, F.453 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.153, B:L.157, B:F.453 Hydrogen bonds: B:N.152, B:C.285, B:Y.445 Water bridges: B:W.160, B:E.251 Salt bridges: B:R.103, B:R.447 2VS.9: 13 residues within 4Å: Chain C: R.103, N.152, L.153, L.156, L.157, W.160, E.251, V.284, C.285, Y.445, R.447, F.453 Ligands: NAD.7 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.153, C:L.157, C:F.453 Hydrogen bonds: C:N.152, C:C.285, C:Y.445, C:Y.445 Water bridges: C:E.251 Salt bridges: C:R.103, C:R.447 2VS.12: 12 residues within 4Å: Chain D: R.103, N.152, L.153, L.157, W.160, E.251, V.284, C.285, Y.445, R.447, F.453 Ligands: NAD.10 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.153, D:L.157, D:F.453 Hydrogen bonds: D:N.152, D:C.285, D:Y.445, D:Y.445 Water bridges: D:E.251 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