SMTL ID : 5kxj.3 (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-hexamer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: L.71, G.76, I.77, C.78 Ligand excluded by PLIP GOL.2: 3 residues within 4Å: Chain A: S.146, Q.149, N.150 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: L.71, G.76, I.77, C.78 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain B: S.146, Q.149, N.150 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain C: L.71, G.76, I.77, C.78 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain C: S.146, Q.149, N.150 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain C: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain D: L.71, G.76, I.77, C.78 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain D: S.146, Q.149, N.150 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain D: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain E: L.71, G.76, I.77, C.78 Ligand excluded by PLIP GOL.42: 3 residues within 4Å: Chain E: S.146, Q.149, N.150 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain E: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 Ligand excluded by PLIP GOL.51: 4 residues within 4Å: Chain F: L.71, G.76, I.77, C.78 Ligand excluded by PLIP GOL.52: 3 residues within 4Å: Chain F: S.146, Q.149, N.150 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain F: Q.212, Y.213, T.214, P.217, N.255, W.440, R.444 Ligand excluded by PLIP

30 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 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: H.81, F.85, D.361 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: L.25, R.26, E.29, W.96, Q.100 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.163, D.164, R.230, L.488, R.491 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: R.234, I.530 Chain C: E.424, R.426 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: R.26, T.92, C.93, W.96, W.400 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: H.81, F.85, D.361 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: L.25, R.26, E.29, W.96, Q.100 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: V.163, D.164, R.230, L.488, R.491 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: E.424, R.426 Chain B: R.234, I.530 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain C: R.26, T.92, C.93, W.96, W.400 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: H.81, F.85, D.361 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: L.25, R.26, E.29, W.96, Q.100 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: V.163, D.164, R.230, L.488, R.491 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: E.424, R.426 Chain C: R.234, I.530 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain D: R.26, T.92, C.93, W.96, W.400 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain D: H.81, F.85, D.361 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain D: L.25, R.26, E.29, W.96, Q.100 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain D: V.163, D.164, R.230, L.488, R.491 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain D: R.234, I.530 Chain F: E.424, R.426 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain E: R.26, T.92, C.93, W.96, W.400 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain E: H.81, F.85, D.361 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain E: L.25, R.26, E.29, W.96, Q.100 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain E: V.163, D.164, R.230, L.488, R.491 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain D: E.424, R.426 Chain E: R.234, I.530 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain F: R.26, T.92, C.93, W.96, W.400 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain F: H.81, F.85, D.361 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain F: L.25, R.26, E.29, W.96, Q.100 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain F: V.163, D.164, R.230, L.488, R.491 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain E: E.424, R.426 Chain F: R.234, I.530 Ligand excluded by PLIP

6 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 SO4.28: 4 residues within 4Å: Chain C: K.198, V.413, H.414, S.415 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.413, C:S.415 Salt bridges: C:K.198 SO4.38: 4 residues within 4Å: Chain D: K.198, V.413, H.414, S.415 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.413, D:S.415 Salt bridges: D:K.198 SO4.48: 4 residues within 4Å: Chain E: K.198, V.413, H.414, S.415 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.413, E:S.415 Salt bridges: E:K.198 SO4.58: 4 residues within 4Å: Chain F: K.198, V.413, H.414, S.415 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.413, F:S.415 Salt bridges: F:K.198

6 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 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain B Hydrogen bonds: D.20, D.20, B:A.18, B:A.19, B:E.375 Water bridges: B:G.20, B:V.376, B:E.394, B:C.395, B:C.395 ASP.30: 8 residues within 4Å: Chain C: G.17, A.18, A.19, G.374, E.375, S.391, L.392, C.395 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:A.18, C:A.19, C:E.375, D.30, D.30 Water bridges: C:G.20, C:Y.352, C:V.376, C:C.395 ASP.40: 8 residues within 4Å: Chain D: G.17, A.18, A.19, G.374, E.375, S.391, L.392, C.395 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:A.18, D:A.19, D:E.375, D.40, D.40 Water bridges: D:G.20, D:V.376, D:E.394, D:C.395, D:C.395 ASP.50: 8 residues within 4Å: Chain E: G.17, A.18, A.19, G.374, E.375, S.391, L.392, C.395 9 PLIP interactions: 2 Ligand-Ligand interactions, 7 interactions with chain E Hydrogen bonds: D.50, D.50, E:A.18, E:A.19, E:E.375 Water bridges: E:G.20, E:Y.352, E:V.376, E:C.395 ASP.60: 8 residues within 4Å: Chain F: G.17, A.18, A.19, G.374, E.375, S.391, L.392, C.395 10 PLIP interactions: 8 interactions with chain F, 2 Ligand-Ligand interactions Hydrogen bonds: F:A.18, F:A.19, F:E.375, D.60, D.60 Water bridges: F:G.20, F:V.376, F:E.394, F:C.395, F: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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

L-aspartate oxidase

Related Entries With Identical Sequence