SMTL ID : 5x8f.2 (1 other biounit)

Ternary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with AMP and its product analogue OSB-NCoA at 1.76 angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

S0N.1: 27 residues within 4Å: Chain A: K.85, L.191, P.192, H.195, I.196, S.197, S.200, 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 27 PLIP interactions: 27 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:S.292, A:Q.293, A:S.388, A:G.389, A:G.390 Water bridges: A:H.195, A:F.218, A:G.263, A:S.284, A:T.288, A:Q.293, A:G.390, A:Y.451 Salt bridges: A:K.204, A:K.420 pi-Stacking: A:W.421, A:W.421 S0N.22: 28 residues within 4Å: Chain B: K.85, L.191, P.192, H.195, I.196, S.197, S.200, 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.23, NA.36 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.196, B:F.218, B:L.260 Hydrogen bonds: B:K.85, 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:H.195, B:H.195, B:F.218, B:S.292, B:S.292 Salt bridges: B:K.204, B:K.420, B:K.450 pi-Stacking: B:W.421, B:W.421

15 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.14, H2O.14, H2O.14 MG.3: 5 residues within 4Å: Chain A: N.178, F.282, T.296, L.297, S.298 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: L.33, H.70, L.202, V.206 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, A:L.202, H2O.5 MG.5: 3 residues within 4Å: Chain A: E.317 Chain B: P.5, M.9 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: E.115 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: E.90, E.397, R.447 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.397, H2O.3, H2O.7 MG.9: 4 residues within 4Å: Chain A: Y.23, E.24, L.214, H.215 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.214 MG.23: 2 residues within 4Å: Chain B: F.218 Ligands: S0N.22 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.218, H2O.30 MG.24: 5 residues within 4Å: Chain B: V.238, Q.239, T.240, G.389, G.390 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.240, H2O.23, H2O.32 MG.25: 1 residues within 4Å: Chain B: E.24 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.24, B:E.24, H2O.30 MG.26: 6 residues within 4Å: Chain B: S.171, T.290, C.291, S.292, Q.293, N.341 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.171, B:T.290, B:Q.293 MG.27: 1 residues within 4Å: Chain B: E.132 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.132, B:E.132, H2O.33, H2O.35, H2O.35 MG.28: 2 residues within 4Å: Chain B: I.318, L.370 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:I.318, H2O.27, H2O.31, H2O.33 MG.29: 3 residues within 4Å: Chain B: E.391, N.392, Y.451 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.391, B:N.392, B:Y.451, H2O.35

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

NA.10: 4 residues within 4Å: Chain A: G.339, P.340, V.342 Ligands: PEG.20 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain A: E.289, Y.346, T.364 Ligand excluded by PLIP NA.12: 3 residues within 4Å: Chain A: R.349, E.350, S.351 Ligand excluded by PLIP NA.13: 3 residues within 4Å: Chain A: K.51, L.75, E.137 Ligand excluded by PLIP NA.14: 1 residues within 4Å: Chain A: R.39 Ligand excluded by PLIP NA.15: 5 residues within 4Å: Chain A: S.383, V.413, S.414, G.415, R.473 Ligand excluded by PLIP NA.16: 3 residues within 4Å: Chain A: E.3, Q.4 Chain B: P.340 Ligand excluded by PLIP NA.17: 3 residues within 4Å: Chain A: T.240, A.243, S.244 Ligand excluded by PLIP NA.18: 1 residues within 4Å: Chain A: A.45 Ligand excluded by PLIP NA.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.31: 4 residues within 4Å: Chain B: T.182, E.183, Y.208 Ligands: PEG.41 Ligand excluded by PLIP NA.32: 1 residues within 4Å: Chain B: R.257 Ligand excluded by PLIP NA.33: 1 residues within 4Å: Chain B: K.344 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Chain B: T.88, H.89, E.446 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain B: K.450, Y.451, R.453 Ligand excluded by PLIP NA.36: 4 residues within 4Å: Chain B: G.263, G.390, N.392 Ligands: S0N.22 Ligand excluded by PLIP NA.37: 1 residues within 4Å: Chain B: E.96 Ligand excluded by PLIP NA.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain B: E.354, A.355, F.357, Q.358 Ligand excluded by PLIP NA.40: 4 residues within 4Å: Chain B: L.403, H.405, P.406, V.408 Ligand excluded by PLIP

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

PEG.19: 9 residues within 4Å: Chain A: R.18, T.182, E.183, Y.208, G.209 Chain B: L.177, N.178, L.179, G.180 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Water bridges: B:L.179, A:R.18, A:T.182 Hydrogen bonds: A:R.18, A:T.182, A:E.183, A:E.183 PEG.20: 8 residues within 4Å: Chain A: D.143, T.164, N.167, V.342, M.343, K.344 Chain B: L.1 Ligands: NA.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.167, A:N.167 Water bridges: A:D.143, A:D.143, A:N.167, B:L.1 PEG.41: 8 residues within 4Å: Chain A: L.177, N.178, L.179, G.180, R.257 Chain B: T.182, E.183 Ligands: NA.31 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.177, B:E.183, B:E.183 Water bridges: A:R.257, B:R.18

1 x CA: CALCIUM ION(Non-covalent)

CA.21: 1 residues within 4Å: Chain A: E.24 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.24, A:E.24

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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