SMTL ID : 3jze.1 (1 other biounit)

1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.41, H.43, K.127, D.275 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.41, A:H.43, A:D.275, H2O.3 ZN.2: 4 residues within 4Å: Chain A: K.127, H.164, H.202 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.164, A:H.202, H2O.3 ZN.8: 6 residues within 4Å: Chain B: H.41, H.43, K.127, D.275 Ligands: ZN.9, ACY.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.41, B:H.43, B:D.275, H2O.25 ZN.9: 5 residues within 4Å: Chain B: K.127, H.164, H.202 Ligands: ZN.8, ACY.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.164, B:H.202, H2O.14, H2O.25 ZN.15: 5 residues within 4Å: Chain C: H.41, H.43, K.127, D.275 Ligands: ZN.16 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.41, C:H.43, C:D.275, H2O.37 ZN.16: 5 residues within 4Å: Chain C: H.41, K.127, H.164, H.202 Ligands: ZN.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.164, C:H.202, H2O.37 ZN.22: 5 residues within 4Å: Chain D: H.41, H.43, K.127, D.275 Ligands: ZN.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.41, D:H.43, D:D.275, H2O.47 ZN.23: 5 residues within 4Å: Chain D: K.127, H.164, H.202 Ligands: ZN.22, ACY.28 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:H.164, D:H.202, ACY.28, H2O.41, H2O.47

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.252 Chain B: R.252 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: R.252 Chain D: R.252 Ligand excluded by PLIP

8 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 6 residues within 4Å: Chain A: C.288, G.289, C.290 Chain B: G.238, G.239 Ligands: BME.5 No protein-ligand interaction detected (PLIP) BME.5: 5 residues within 4Å: Chain A: T.135, H.279, R.283, C.290 Ligands: BME.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.279, A:R.283 BME.10: 6 residues within 4Å: Chain A: G.238, G.239 Chain B: C.288, G.289, C.290 Ligands: BME.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.289 BME.11: 3 residues within 4Å: Chain B: H.279, C.290 Ligands: BME.10 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.279, B:R.283 BME.18: 6 residues within 4Å: Chain C: C.288, G.289, C.290 Chain D: G.238, G.239 Ligands: BME.19 No protein-ligand interaction detected (PLIP) BME.19: 5 residues within 4Å: Chain C: T.135, H.279, R.283, C.290 Ligands: BME.18 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.283, C:R.283 BME.24: 6 residues within 4Å: Chain C: G.238, G.239 Chain D: C.288, G.289, C.290 Ligands: BME.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.289 BME.25: 4 residues within 4Å: Chain D: H.279, C.290 Ligands: BME.24, ACY.27 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 6 residues within 4Å: Chain A: K.197, D.217, Y.218, Q.326, F.327, G.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.197, A:Y.218 Water bridges: A:G.329 PGE.20: 6 residues within 4Å: Chain C: K.197, D.217, Y.218, Q.326, F.327, G.329 No protein-ligand interaction detected (PLIP)

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 8 residues within 4Å: Chain A: H.43, R.45, N.69, T.134, T.135, A.277, H.279, A.291 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.277 Hydrogen bonds: A:N.69, A:T.135 Salt bridges: A:H.43, A:R.45, A:H.279 ACY.13: 7 residues within 4Å: Chain B: H.43, R.45, N.69, A.277, H.279, A.291 Ligands: ACY.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.69 Salt bridges: B:H.43, B:R.45, B:H.279 ACY.14: 7 residues within 4Å: Chain B: N.69, K.127, Y.129, H.164 Ligands: ZN.8, ZN.9, ACY.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.129 Water bridges: B:L.247 Salt bridges: B:H.164 ACY.21: 8 residues within 4Å: Chain C: H.43, R.45, N.69, T.134, T.135, A.277, H.279, A.291 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.277 Hydrogen bonds: C:N.69, C:A.291 Salt bridges: C:H.43, C:R.45, C:H.279 ACY.27: 7 residues within 4Å: Chain D: H.43, R.45, N.69, H.279, A.291 Ligands: BME.25, ACY.28 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.69 Salt bridges: D:H.43, D:R.45, D:H.279 ACY.28: 6 residues within 4Å: Chain D: N.69, K.127, Y.129, H.164 Ligands: ZN.23, ACY.27 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.129 Water bridges: D:L.247, D:L.247 Salt bridges: D:H.164

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 6 residues within 4Å: Chain B: K.197, D.217, Y.218, Q.326, F.327, G.329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.197 Water bridges: B:G.329 PG4.26: 7 residues within 4Å: Chain D: G.158, K.197, D.217, Y.218, Q.326, F.327, G.329 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.197 Water bridges: D:G.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. TO BE PUBLISHED

Release Date

2009-09-29

Peptides

Dihydroorotase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydroorotase

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