SMTL ID : 1qxo.1

Crystal structure of Chorismate synthase complexed with oxidized FMN and EPSP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

9 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.1: 2 residues within 4Å: Chain A: D.170, E.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.170, A:D.170, A:E.173 NCO.2: 3 residues within 4Å: Chain A: R.120, D.122 Chain C: E.372 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.120, A:D.122, A:D.122, C:E.372, C:E.372 Water bridges: C:K.66 NCO.3: 2 residues within 4Å: Chain A: N.387, Y.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.387, A:N.387, A:Y.388 NCO.9: 3 residues within 4Å: Chain B: A.151, E.152, D.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.152, B:E.152, B:D.154 Water bridges: B:K.375 NCO.10: 2 residues within 4Å: Chain B: N.387, Y.388 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.387, B:N.387, B:N.387 NCO.14: 3 residues within 4Å: Chain C: N.387, Y.388 Chain D: H.328 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Water bridges: D:H.328, C:N.387 Hydrogen bonds: C:N.387, C:Y.388, C:Y.388, C:Y.388 NCO.15: 5 residues within 4Å: Chain C: E.168, E.263 Chain D: Y.266 Ligands: FMN.18, FMN.25 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.168, C:E.263, C:E.263, C:E.263, C:E.263, D:Y.266 Water bridges: C:E.168 NCO.20: 5 residues within 4Å: Chain C: Y.266 Chain D: E.168, E.263 Ligands: FMN.18, FMN.25 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.168, D:E.168, D:E.168, D:E.263, D:E.263, D:E.263 Water bridges: D:R.307 NCO.21: 2 residues within 4Å: Chain D: N.387, Y.388 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.388 Water bridges: D:Y.388, D:Y.388

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

EDO.4: 8 residues within 4Å: Chain A: V.227, Y.284, R.286, N.300, T.385 Chain B: L.113, V.114, I.117 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.286, A:R.286 Water bridges: A:Y.284, A:Y.284, A:Y.284 EDO.5: 5 residues within 4Å: Chain A: Y.3, L.4 Chain C: R.2, Y.3, L.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.2, C:R.2 Water bridges: A:Y.3, A:Y.3, C:Y.3, C:Y.3 EDO.6: 7 residues within 4Å: Chain A: G.20, I.21, P.22, S.368, D.369 Chain C: Y.119 Chain D: R.237 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:I.21, A:D.369, D:R.237, D:R.237 EDO.11: 6 residues within 4Å: Chain A: I.117 Chain B: V.227, Y.284, R.286, N.300, T.385 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.286, B:R.286 Water bridges: B:Y.284, B:Y.284, B:Y.284, B:Y.284 EDO.16: 6 residues within 4Å: Chain C: V.227, Y.284, R.286, N.300, T.385 Chain D: I.117 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.286, C:R.286, C:N.300 Water bridges: C:Y.284, C:Y.284 EDO.22: 7 residues within 4Å: Chain C: L.113, I.117 Chain D: V.227, Y.284, R.286, N.300, T.385 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.284, D:R.286, D:R.286 EDO.23: 5 residues within 4Å: Chain B: R.2, Y.3, L.4 Chain D: R.2, L.4 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Water bridges: B:R.2, B:R.2, B:Y.3, B:Y.3, D:Y.3, D:Y.3 Hydrogen bonds: D:R.2

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.7: 17 residues within 4Å: Chain A: R.45, G.109, H.110, S.131, A.133, N.251, A.252, M.310, K.311, I.313, P.314, T.315, A.342, A.346 Chain B: E.295, G.296 Ligands: EPS.8 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:G.296, A:H.110, A:S.131, A:A.133, A:I.250, A:N.251, A:A.252, A:K.311, A:T.315, A:T.315, A:T.315 Water bridges: B:K.238, B:G.297, B:G.297, A:R.45, A:F.253, A:D.339 Hydrophobic interactions: A:A.133, A:N.251, A:A.342 Salt bridges: A:K.311 FMN.12: 20 residues within 4Å: Chain A: E.295, G.296 Chain B: R.45, G.109, H.110, S.131, A.133, N.251, A.252, M.310, K.311, I.313, P.314, T.315, S.338, D.339, A.342, A.345, A.346 Ligands: EPS.13 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.133, B:N.251, B:A.342, B:A.345, B:A.346 Hydrogen bonds: B:H.110, B:A.133, B:N.251, B:A.252, B:K.311, B:T.315, B:S.338, B:S.338, B:D.339, A:G.296 Water bridges: B:R.45, B:F.253, A:G.297, A:G.297 Salt bridges: B:K.311 FMN.17: 20 residues within 4Å: Chain C: R.45, G.109, H.110, S.131, A.133, I.250, N.251, A.252, M.310, K.311, I.313, P.314, T.315, S.338, D.339, A.342, A.345 Chain D: E.295, G.296 Ligands: EPS.19 23 PLIP interactions: 19 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:A.133, C:I.250, C:N.251, C:A.342, C:A.345 Hydrogen bonds: C:H.110, C:H.110, C:A.133, C:N.251, C:A.252, C:K.311, C:T.315, C:T.315, C:S.338, C:S.338, C:D.339, D:G.296 Water bridges: C:R.45, C:F.253, D:K.238, D:G.297, D:G.297 Salt bridges: C:K.311 FMN.18: 7 residues within 4Å: Chain C: F.262, E.263, Y.266 Chain D: E.168 Ligands: NCO.15, NCO.20, FMN.25 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.266, C:Y.266 Water bridges: C:F.262 Hydrogen bonds: D:E.168 FMN.24: 19 residues within 4Å: Chain C: E.295, G.296 Chain D: R.45, G.109, H.110, S.131, A.133, N.251, A.252, M.310, K.311, I.313, P.314, T.315, S.338, D.339, A.342, A.345 Ligands: EPS.26 23 PLIP interactions: 19 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.133, D:N.251, D:A.342, D:A.345 Hydrogen bonds: D:H.110, D:S.131, D:A.133, D:I.250, D:N.251, D:A.252, D:F.253, D:K.311, D:T.315, D:T.315, D:S.338, D:S.338, D:D.339, C:G.296 Water bridges: D:R.45, C:K.238, C:G.297, C:G.297 Salt bridges: D:K.311 FMN.25: 7 residues within 4Å: Chain C: E.168 Chain D: F.262, E.263, Y.266 Ligands: NCO.15, FMN.18, NCO.20 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:E.263, D:Y.266, D:Y.266 Water bridges: D:E.257, D:E.263 pi-Stacking: D:Y.266

4 x EPS: 5-[(1-CARBOXYVINYL)OXY]-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID(Non-covalent)

EPS.8: 11 residues within 4Å: Chain A: H.10, R.39, R.45, R.48, M.49, H.110, S.132, A.133, R.134, T.137 Ligands: FMN.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.48 Hydrogen bonds: A:R.45, A:R.48, A:A.133 Water bridges: A:S.9, A:S.9, A:H.10, A:R.107, A:R.107 Salt bridges: A:H.10, A:R.39, A:R.45, A:H.110, A:R.134 EPS.13: 11 residues within 4Å: Chain B: H.10, R.39, R.45, R.48, M.49, H.110, S.132, A.133, R.134, R.337 Ligands: FMN.12 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.48, B:R.134 Hydrogen bonds: B:R.45, B:A.133, B:R.337, B:R.337 Water bridges: B:S.9, B:S.9, B:R.48, B:R.48, B:D.339 Salt bridges: B:H.10, B:R.39, B:R.45, B:R.48, B:H.110, B:R.134, B:R.337 EPS.19: 12 residues within 4Å: Chain C: H.10, R.39, R.45, R.48, M.49, H.110, S.132, A.133, R.134, T.137, R.337 Ligands: FMN.17 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:R.48, C:R.134 Hydrogen bonds: C:S.9, C:S.9, C:R.45, C:R.48, C:A.133, C:R.337 Water bridges: C:R.48, C:R.48, C:R.107, C:H.110, C:D.339, C:D.339 Salt bridges: C:H.10, C:R.39, C:R.45, C:H.110, C:R.134, C:R.337 EPS.26: 12 residues within 4Å: Chain D: H.10, R.39, R.45, R.48, M.49, H.110, S.132, A.133, R.134, T.137, R.337 Ligands: FMN.24 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:R.48 Hydrogen bonds: D:S.9, D:S.9, D:R.45, D:A.133, D:R.337 Water bridges: D:R.48, D:R.48, D:R.48, D:R.107, D:E.336, D:E.336, D:R.337 Salt bridges: D:H.10, D:R.39, D:R.45, D:R.48, D:H.110, D:R.134, D:R.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maclean, J. et al., The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction. Structure (2003)

Release Date

2003-12-23

Peptides

Chorismate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Chorismate synthase