SMTL ID : 5i39.1

High resolution structure of L-amino acid deaminase from Proteus vulgaris with the deletion of the specific insertion sequence

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 36 residues within 4Å: Chain A: V.43, G.44, G.46, I.47, L.48, V.66, E.67, K.68, E.74, Q.75, S.76, R.78, F.79, Y.80, G.81, Q.82, C.208, A.209, A.210, A.238, G.239, G.240, W.242, F.246, Q.261, Q.263, G.346, M.348, T.373, G.374, W.375, G.376, M.377, T.378 Ligands: EDO.3, EDO.10 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.79, A:Q.261, A:Q.263 Hydrogen bonds: A:L.48, A:K.68, A:Q.75, A:Q.75, A:S.76, A:S.76, A:Y.80, A:G.81, A:Q.82, A:Q.82, A:A.210, A:A.210, A:G.240, A:T.373, A:G.376, A:T.378, A:T.378 Water bridges: A:G.46, A:G.46, A:E.67, A:K.68, A:G.73, A:E.74, A:E.74, A:E.74 pi-Stacking: A:W.375

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: G.25, F.26, N.70, I.71, A.72, G.73, S.77, F.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:S.77 Water bridges: A:N.70 EDO.3: 4 residues within 4Å: Chain A: K.68, R.211, W.242 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.211 EDO.4: 4 residues within 4Å: Chain A: P.125, D.127, E.128, I.174 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.126 EDO.5: 3 residues within 4Å: Chain A: L.213, T.215, L.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.215, A:T.215 Water bridges: A:L.213 EDO.6: 4 residues within 4Å: Chain A: N.322, L.325, E.326, K.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.322 Water bridges: A:K.329, A:K.329 EDO.7: 4 residues within 4Å: Chain A: V.301, E.354, G.374, W.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.301, A:E.354 EDO.8: 9 residues within 4Å: Chain A: E.123, V.124, P.125, L.126, D.130, A.278, L.279, P.280, F.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.130, A:D.130 EDO.9: 4 residues within 4Å: Chain A: R.117, E.287, Q.288, A.289 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.119, A:E.287, A:E.287, A:Q.288, A:A.289 EDO.10: 8 residues within 4Å: Chain A: Q.261, V.299, I.300, V.301, M.348, G.374, W.375 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.261, A:V.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ju, Y. et al., Crystal structure of a membrane-bound l-amino acid deaminase from Proteus vulgaris. J.Struct.Biol. (2016)

Release Date

2016-08-03

Peptides

L-amino acid deaminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L-amino acid deaminase