SMTL ID : 5klm.1

Crystal structure of 2-hydroxymuconate-6-semialdehyde derived intermediate in NAD(+)-bound 2-aminomuconate 6-semialdehyde dehydrogenase N169D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 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, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.187, A:L.194, A:T.265 Hydrogen bonds: A:S.186, A:W.188, A:K.212, A:E.215, A:E.267, A:T.270, A:L.289, A:E.424 NAD.3: 27 residues within 4Å: Chain B: 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, F.264, T.265, G.266, E.267, T.270, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.187, B:L.194, B:T.265 Hydrogen bonds: B:S.186, B:W.188, B:K.212, B:E.215, B:E.267, B:T.270, B:T.270, B:E.288, B:L.289, B:E.424 NAD.5: 30 residues within 4Å: Chain C: 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, I.274, E.288, L.289, G.290, C.322, E.424, F.426, L.452, F.490 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:P.187, C:L.194, C:T.265 Hydrogen bonds: C:S.186, C:K.212, C:E.215, C:K.246, C:E.267, C:T.270, C:T.270, C:E.288, C:L.289, C:E.424 Water bridges: C:W.188, C:G.245, C:E.424, C:E.424 NAD.7: 29 residues within 4Å: Chain D: 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 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:P.187, D:L.194, D:T.265 Hydrogen bonds: D:S.186, D:K.212, D:E.215, D:E.267, D:E.267, D:T.270, D:L.289, D:E.424 Water bridges: D:E.267, D:E.424

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

NA.2: 4 residues within 4Å: Chain A: N.57, I.58, D.125, E.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.58, A:E.216 NA.4: 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:E.216 NA.6: 4 residues within 4Å: Chain C: N.57, I.58, D.125, E.216 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.58, C:D.125 NA.8: 4 residues within 4Å: Chain D: N.57, I.58, D.125, E.216 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.57, D:I.58

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
C

D
D

2-aminomuconate 6-semialdehyde dehydrogenase

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