SMTL ID : 5kxj.2 (2 other biounits)

Crystal Structure of L-Aspartate Oxidase from Salmonella typhimurium in the Complex with Substrate L-Aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: L.71, G.76, I.77, C.78 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.76, A:C.78 GOL.2: 3 residues within 4Å: Chain A: S.146, Q.149, N.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.146, A:N.150 GOL.3: 7 residues within 4Å: Chain A: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.214, A:T.214, A:R.444 GOL.11: 4 residues within 4Å: Chain B: L.71, G.76, I.77, C.78 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.76, B:C.78 GOL.12: 3 residues within 4Å: Chain B: S.146, Q.149, N.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.146, B:N.150 GOL.13: 7 residues within 4Å: Chain B: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.214, B:T.214, B:R.444

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

EDO.4: 5 residues within 4Å: Chain A: R.26, T.92, C.93, W.96, W.400 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.26, A:R.26 EDO.5: 3 residues within 4Å: Chain A: H.81, F.85, D.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.81 EDO.6: 5 residues within 4Å: Chain A: L.25, R.26, E.29, W.96, Q.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.100 Water bridges: A:R.147 EDO.7: 5 residues within 4Å: Chain A: V.163, D.164, R.230, L.488, R.491 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.491 Water bridges: A:R.230 EDO.9: 2 residues within 4Å: Chain A: R.234, I.530 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.234, A:R.234 EDO.14: 5 residues within 4Å: Chain B: R.26, T.92, C.93, W.96, W.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.26, B:R.26 EDO.15: 3 residues within 4Å: Chain B: H.81, F.85, D.361 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.361 EDO.16: 5 residues within 4Å: Chain B: L.25, R.26, E.29, W.96, Q.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.100 Water bridges: B:R.147 EDO.17: 5 residues within 4Å: Chain B: V.163, D.164, R.230, L.488, R.491 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.491 Water bridges: B:R.230 EDO.19: 2 residues within 4Å: Chain B: R.234, I.530 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.234, B:R.234

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

SO4.8: 4 residues within 4Å: Chain A: K.198, V.413, H.414, S.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.413, A:S.415 Salt bridges: A:K.198 SO4.18: 4 residues within 4Å: Chain B: K.198, V.413, H.414, S.415 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.413, B:S.415 Salt bridges: B:K.198

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.10: 8 residues within 4Å: Chain A: G.17, A.18, A.19, G.374, E.375, S.391, L.392, C.395 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:A.18, A:A.19, A:E.375, D.10, D.10 Water bridges: A:G.20, A:Y.352, A:V.376, A:C.395 ASP.20: 8 residues within 4Å: Chain B: G.17, A.18, A.19, G.374, E.375, S.391, L.392, C.395 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:A.18, B:A.19, B:E.375, D.20, D.20 Water bridges: B:G.20, B:Y.352, B:V.376, B:C.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of L-Aspartate Oxidase from Salmonella typhimurium in the Complex with Substrate L-Aspartate. To Be Published

Release Date

2016-08-03

Peptides

L-aspartate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

L-aspartate oxidase

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