SMTL ID : 5klk.1

Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169D in complex with NAD+ and 2-hydroxymuconate-6-semialdehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: I.185, S.186, P.187, W.188, D.189, L.194, K.212, S.214, E.215, F.244, G.245, K.246, G.250, E.251, T.254, F.264, T.265, G.266, E.267, T.270, T.273, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 Ligands: 6OH.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.194, A:T.265 Hydrogen bonds: A:S.186, A:W.188, A:K.212, A:E.215, A:K.246, A:E.267, A:E.267, A:T.270, A:L.289, A:E.424 Water bridges: A:W.188, A:S.268 NAD.4: 30 residues within 4Å: Chain B: I.185, S.186, P.187, W.188, D.189, L.194, K.212, P.213, S.214, E.215, F.244, G.245, K.246, G.250, E.251, F.264, T.265, G.266, E.267, T.270, T.273, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 Ligands: 6OH.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.194, B:T.265 Hydrogen bonds: B:S.186, B:W.188, B:K.212, B:E.215, B:E.267, B:E.267, B:T.270, B:T.270, B:E.288, B:L.289, B:E.424 Water bridges: B:W.188, B:S.268 NAD.7: 30 residues within 4Å: Chain C: I.185, S.186, P.187, W.188, D.189, L.194, K.212, P.213, S.214, E.215, F.244, G.245, K.246, G.250, E.251, T.254, F.264, T.265, G.266, E.267, T.270, T.273, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.194, C:T.265 Hydrogen bonds: C:S.186, C:W.188, C:K.212, C:E.215, C:K.246, C:E.267, C:T.270, C:L.289, C:E.424 Water bridges: C:G.245, C:E.267 NAD.8: 31 residues within 4Å: Chain D: I.185, S.186, P.187, W.188, D.189, L.194, K.212, P.213, S.214, E.215, F.244, G.245, K.246, G.250, E.251, T.254, F.264, T.265, G.266, E.267, T.270, T.273, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 Ligands: 6OH.9 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:P.187, D:L.194, D:T.265 Hydrogen bonds: D:S.186, D:W.188, D:K.212, D:E.215, D:K.246, D:E.267, D:T.270, D:T.270, D:L.289, D:E.424 Water bridges: D:W.188, D:T.254, D:S.268

3 x 6OH: (2E,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid(Non-covalent)

6OH.2: 11 residues within 4Å: Chain A: R.140, L.190, L.193, L.194, W.197, C.322, L.323, Y.482, R.484, F.490 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.190, A:Y.482 Hydrogen bonds: A:R.140, A:R.140, A:Y.482, A:R.484 Salt bridges: A:R.140, A:R.484 6OH.5: 11 residues within 4Å: Chain B: R.140, L.190, L.193, L.194, W.197, C.322, L.323, Y.482, R.484, F.490 Ligands: NAD.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.190, B:Y.482 Hydrogen bonds: B:R.140, B:R.140, B:Y.482, B:Y.482 Salt bridges: B:R.140, B:R.484 6OH.9: 10 residues within 4Å: Chain D: R.140, L.193, L.194, W.197, C.322, L.323, Y.482, R.484, F.490 Ligands: NAD.8 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.323, D:Y.482, D:F.490 Hydrogen bonds: D:R.140, D:R.140, D:Y.482, D:Y.482 Salt bridges: D:R.140, D:R.484

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

NA.3: 4 residues within 4Å: Chain A: I.58, D.125, E.216, I.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.58, A:E.216 NA.6: 4 residues within 4Å: Chain B: N.57, I.58, D.125, E.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.58, B:D.125 NA.10: 4 residues within 4Å: Chain D: I.58, D.125, E.216, I.365 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., A Pitcher-and-Catcher Mechanism Drives Endogenous Substrate Isomerization by a Dehydrogenase in Kynurenine Metabolism. J.Biol.Chem. (2016)

Release Date

2016-11-09

Peptides

2-aminomuconate 6-semialdehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

2-aminomuconate 6-semialdehyde dehydrogenase

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