SMTL ID : 7bzv.1

Crystal structure of 2-aminomuconic 6-semialdehyde dehydrogenase from Pseudomonas species AP-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: W.153, D.181, I.330, S.331, K.333, H.334 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.331, A:K.333, A:H.334 Water bridges: A:D.181, A:D.181 GOL.7: 4 residues within 4Å: Chain B: S.340, Y.341, L.344, R.384 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.384, B:R.384 Water bridges: B:S.340, B:S.340 GOL.8: 8 residues within 4Å: Chain B: W.153, S.179, E.180, D.181, I.330, S.331, K.333, H.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.181, B:D.181, B:S.331, B:K.333 Water bridges: B:S.179 GOL.10: 6 residues within 4Å: Chain C: W.153, D.181, I.330, S.331, K.333, H.334 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.331, C:K.333, C:H.334 Water bridges: C:D.181, C:D.181 GOL.16: 4 residues within 4Å: Chain D: S.340, Y.341, L.344, R.384 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.384, D:R.384 Water bridges: D:S.340, D:S.340 GOL.17: 8 residues within 4Å: Chain D: W.153, S.179, E.180, D.181, I.330, S.331, K.333, H.334 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.181, D:S.331, D:K.333 Water bridges: D:S.179

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 8 residues within 4Å: Chain A: H.50, D.223, I.224, S.225, K.248 Chain B: R.414, R.437, G.459 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.248 Water bridges: A:S.225, A:S.225, A:S.225 PEG.3: 11 residues within 4Å: Chain A: I.150, K.177, G.210, P.211, G.215, E.216, S.219, F.229, T.235, T.238, I.239 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.177 PEG.4: 6 residues within 4Å: Chain A: N.112, R.449, D.450, L.451, R.452 Chain B: L.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.112, A:L.451, A:R.452 Water bridges: A:N.112, A:R.452 PEG.5: 7 residues within 4Å: Chain A: M.469, H.470, N.473 Chain B: D.123, M.469, H.470, N.473 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.123, B:N.473, A:N.473 Water bridges: A:M.469 PEG.9: 6 residues within 4Å: Chain A: L.127 Chain B: N.112, D.450, L.451, R.452 Chain C: A.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.450, B:L.451 Water bridges: B:N.112, B:N.112, B:N.112 PEG.11: 8 residues within 4Å: Chain C: H.50, D.223, I.224, S.225, K.248 Chain D: R.414, R.437, G.459 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.248 Water bridges: C:S.225, C:S.225, C:S.225 PEG.12: 11 residues within 4Å: Chain C: I.150, K.177, G.210, P.211, G.215, E.216, S.219, F.229, T.235, T.238, I.239 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.177 PEG.13: 6 residues within 4Å: Chain C: N.112, R.449, D.450, L.451, R.452 Chain D: L.127 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.112, C:L.451, C:R.452 Water bridges: C:N.112, C:R.452 PEG.14: 7 residues within 4Å: Chain C: M.469, H.470, N.473 Chain D: D.123, M.469, H.470, N.473 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.473, D:D.123, D:N.473 Water bridges: C:M.469 PEG.18: 6 residues within 4Å: Chain A: A.63 Chain C: L.127 Chain D: N.112, D.450, L.451, R.452 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.450, D:L.451 Water bridges: D:N.112, D:N.112, D:N.112

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 8 residues within 4Å: Chain A: R.414, G.459 Chain B: H.50, P.222, D.223, I.224, S.225, K.248 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.414, B:I.224, B:S.225 Water bridges: A:G.459, B:K.248 Salt bridges: B:K.248 SO4.15: 8 residues within 4Å: Chain C: R.414, G.459 Chain D: H.50, P.222, D.223, I.224, S.225, K.248 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.414, D:I.224, D:S.225 Water bridges: C:G.459, D:K.248 Salt bridges: D:K.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Q. et al., The tetrameric assembly of 2-aminomuconic 6-semialdehyde dehydrogenase is a functional requirement of cofactor NAD + binding. Environ.Microbiol. (2021)

Release Date

2021-04-28

Peptides

2-aminomuconic 6-semialdehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-aminomuconic 6-semialdehyde dehydrogenase