SMTL ID : 5gtd.1

o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis in Complex with the Acyl-adenylate Intermediate OSB-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.21, Y.211 Chain B: L.180 Ligand excluded by PLIP CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain B: S.174, T.293, C.294, S.295, Q.296, N.344 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: N.181, T.299, L.300, S.301, E.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.299, A:S.301, A:S.301

2 x A: ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

A.5: 15 residues within 4Å: Chain A: S.155, H.198, G.266, G.267, P.268, S.287, Y.288, G.289, M.290, T.291, D.369, V.381, R.384, K.473 Ligands: OSB.6 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.266, A:S.287, A:G.289, A:T.291, A:T.291, A:D.369, A:R.384, A:K.473, B:G.266, B:S.287, B:T.291, B:D.369 Water bridges: A:S.287 Salt bridges: A:H.198, A:K.473 pi-Stacking: A:Y.288, B:Y.288 A.10: 11 residues within 4Å: Chain B: G.266, P.268, S.287, Y.288, G.289, M.290, T.291, D.369, V.381, R.384 Ligands: OSB.11 Protein-ligand interaction information (PLIP) not available

2 x OSB: 2-SUCCINYLBENZOATE(Non-covalent)

OSB.6: 15 residues within 4Å: Chain A: H.198, I.199, S.200, S.239, A.240, L.263, G.265, G.266, S.287, G.289, M.290, T.291, S.295, Q.296 Ligands: A.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.263 Hydrogen bonds: A:S.287, A:T.291, A:T.291, A:Q.296 Salt bridges: A:H.198, A:K.207, A:K.473 OSB.11: 11 residues within 4Å: Chain B: L.194, I.199, S.200, A.240, L.263, G.265, G.289, M.290, S.295, Q.296 Ligands: A.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.194, B:I.199, B:L.263 Hydrogen bonds: B:S.287, B:S.287, B:G.289, B:T.291, B:Q.296, B:Q.296

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 6 residues within 4Å: Chain A: F.317, S.318 Chain B: Q.7, P.8, W.10, Q.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.8

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 7 residues within 4Å: Chain A: L.180, N.181 Chain B: R.21, I.184, T.185, E.186, Y.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.21, B:R.21 pi-Cation interactions: B:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate. Biochemistry (2016)

Release Date

2017-01-04

Peptides

2-succinylbenzoate--CoA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-succinylbenzoate--CoA ligase

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