SMTL ID : 1sjc.1

x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: K.161, K.163, D.189, N.191, E.214, D.239 Ligands: SMG.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.189, A:E.214, A:D.239, H2O.185 MG.2: 8 residues within 4Å: Chain B: K.161, K.163, D.189, N.191, E.214, D.239, K.263 Ligands: SMG.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.189, B:E.214, B:D.239, H2O.228 MG.3: 7 residues within 4Å: Chain C: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: SMG.7 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.189, C:E.214, C:D.239, H2O.696 MG.4: 7 residues within 4Å: Chain D: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: SMG.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.189, D:E.214, D:D.239, H2O.884 MG.9: 7 residues within 4Å: Chain E: K.161, K.163, D.189, N.191, E.214, D.239 Ligands: SMG.13 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.189, E:E.214, E:D.239, H2O.1080 MG.10: 8 residues within 4Å: Chain F: K.161, K.163, D.189, N.191, E.214, D.239, K.263 Ligands: SMG.14 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.189, F:E.214, F:D.239, H2O.1123 MG.11: 7 residues within 4Å: Chain G: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: SMG.15 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.189, G:E.214, G:D.239, H2O.1591 MG.12: 7 residues within 4Å: Chain H: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: SMG.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.189, H:E.214, H:D.239, H2O.1779

8 x SMG: N-SUCCINYL METHIONINE(Non-covalent)

SMG.5: 19 residues within 4Å: Chain A: F.19, T.21, F.23, M.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, D.316, F.323 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.293, A:F.323 Hydrogen bonds: A:S.135, A:K.161, A:K.163, A:N.191, A:N.261, A:K.263, A:G.291, A:G.291, A:I.293 Water bridges: A:N.191, A:G.291, A:E.294, A:R.299, A:R.299 Salt bridges: A:K.161, A:K.163, A:K.263, A:R.299 SMG.6: 20 residues within 4Å: Chain B: F.19, F.23, Q.26, M.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, E.294, D.316, F.323 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.293, B:D.316, B:F.323 Hydrogen bonds: B:S.135, B:K.161, B:K.163, B:N.191, B:K.263, B:G.291, B:G.291, B:I.293 Water bridges: B:N.191, B:N.261, B:G.291, B:M.292, B:R.299, B:R.299 Salt bridges: B:K.161, B:K.163, B:K.263 SMG.7: 19 residues within 4Å: Chain C: F.19, Q.26, M.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, E.294, D.316, F.323 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:D.316, C:F.323 Hydrogen bonds: C:S.135, C:K.161, C:K.163, C:N.191, C:N.191, C:G.291, C:G.291, C:I.293, C:E.294, C:D.316 Water bridges: C:E.214, C:N.261, C:G.291, C:R.299, C:R.299, C:S.318 Salt bridges: C:K.161, C:K.163, C:K.263, C:R.299 SMG.8: 18 residues within 4Å: Chain D: F.19, F.23, Q.26, M.50, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, D.316, F.323 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.293, D:F.323 Hydrogen bonds: D:S.135, D:K.161, D:N.191, D:K.263, D:G.291, D:G.291, D:I.293 Water bridges: D:N.191, D:G.291 Salt bridges: D:K.161, D:K.163, D:K.263, D:R.299 SMG.13: 19 residues within 4Å: Chain E: F.19, T.21, F.23, M.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, D.316, F.323 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:I.293, E:F.323 Hydrogen bonds: E:S.135, E:K.161, E:K.163, E:N.191, E:N.261, E:K.263, E:G.291, E:G.291, E:I.293 Water bridges: E:N.191, E:G.291, E:E.294, E:R.299, E:R.299 Salt bridges: E:K.161, E:K.163, E:K.263, E:R.299 SMG.14: 20 residues within 4Å: Chain F: F.19, F.23, Q.26, M.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, E.294, D.316, F.323 Ligands: MG.10 21 PLIP interactions: 21 interactions with chain F Hydrophobic interactions: F:I.293, F:D.316, F:F.323 Hydrogen bonds: F:S.135, F:K.161, F:K.163, F:N.191, F:D.239, F:K.263, F:G.291, F:G.291, F:I.293 Water bridges: F:N.191, F:G.291, F:M.292, F:R.299, F:R.299, F:D.316 Salt bridges: F:K.161, F:K.163, F:K.263 SMG.15: 19 residues within 4Å: Chain G: F.19, Q.26, M.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, E.294, D.316, F.323 Ligands: MG.11 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:D.316, G:F.323 Hydrogen bonds: G:S.135, G:K.161, G:K.163, G:N.191, G:N.191, G:G.291, G:G.291, G:I.293 Water bridges: G:N.261, G:G.291, G:R.299, G:R.299, G:S.318 Salt bridges: G:K.161, G:K.163, G:K.263, G:R.299 SMG.16: 18 residues within 4Å: Chain H: F.19, F.23, Q.26, M.50, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, G.291, M.292, I.293, D.316, F.323 Ligands: MG.12 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:I.293, H:F.323 Hydrogen bonds: H:S.135, H:K.161, H:N.191, H:N.191, H:D.239, H:K.263, H:G.291, H:G.291, H:I.293 Water bridges: H:N.191, H:G.291 Salt bridges: H:K.161, H:K.163, H:K.263, H:R.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis. Biochemistry (2004)

Release Date

2004-06-01

Peptides

N-acylamino acid racemase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

N-acylamino acid racemase

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