SMTL ID : 5x8g.2 (1 other biounit)

Binary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with its product analogue OSB-NCoA at 1.90 angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x S0N: o-succinylbenzoyl-N-coenzyme A(Non-covalent)

S0N.1: 29 residues within 4Å: Chain A: K.85, L.191, P.192, H.195, I.196, S.197, S.200, R.217, F.218, A.237, V.238, M.241, L.260, G.262, G.263, G.286, M.287, S.292, Q.293, S.388, G.389, G.390, E.391, K.420, W.421, K.450, Y.451 Ligands: MG.2, CA.5 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:I.196, A:F.218, A:V.238, A:L.260 Hydrogen bonds: A:K.85, A:K.85, A:I.196, A:S.197, A:S.197, A:S.200, A:Q.293, A:S.388, A:G.389, A:G.390 Water bridges: A:R.217, A:R.217, A:R.217, A:R.217, A:F.218, A:S.244, A:S.244, A:G.263, A:S.284, A:T.288, A:S.292, A:S.292, A:G.390 Salt bridges: A:K.204, A:R.217, A:R.217, A:K.420 pi-Stacking: A:W.421, A:W.421 S0N.8: 26 residues within 4Å: Chain B: K.85, L.191, P.192, H.195, I.196, S.197, F.218, A.237, V.238, M.241, L.260, G.262, G.263, G.286, M.287, S.292, Q.293, S.388, G.389, G.390, E.391, K.420, W.421, K.450, Y.451 Ligands: MG.9 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:I.196, B:F.218, B:L.260 Hydrogen bonds: B:K.85, B:I.196, B:S.197, B:S.197, B:S.200, B:Q.293, B:S.388, B:G.389, B:G.390, B:K.450 Water bridges: B:K.85, B:K.85, B:K.85, B:K.85, B:H.195, B:H.195, B:F.218, B:G.263, B:S.284, B:S.292, B:Q.293, B:G.390 Salt bridges: B:K.204, B:K.420, B:K.450 pi-Stacking: B:W.421, B:W.421

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: F.218 Ligands: S0N.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.218, H2O.12, H2O.13, H2O.14 MG.3: 1 residues within 4Å: Chain A: T.27 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.27, H2O.6, H2O.12 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: F.218 Ligands: S0N.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.218, H2O.27 MG.10: 4 residues within 4Å: Chain B: K.319, M.336, Q.358, W.361 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.358

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.5: 5 residues within 4Å: Chain A: M.149, H.195, I.196, T.288 Ligands: S0N.1 No protein-ligand interaction detected (PLIP) CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: E.3, Y.139, Q.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.3, A:Q.141 NA.7: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.139 Water bridges: B:E.317 NA.12: 2 residues within 4Å: Chain B: E.354, F.357 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.357

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

PEG.13: 6 residues within 4Å: Chain A: L.179, G.180, T.182, R.257 Chain B: T.182, E.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.183 Water bridges: B:T.182 PEG.14: 8 residues within 4Å: Chain A: I.181, T.182, E.183 Chain B: N.178, L.179, G.180, T.182, R.257 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.183, B:N.178 Water bridges: B:R.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode. J. Biol. Chem. (2017)

Release Date

2017-06-07

Peptides

2-succinylbenzoate--CoA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

2-succinylbenzoate--CoA ligase

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