SMTL ID : 5x8f.1 (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 Compare

Method

X-RAY DIFFRACTION 1.76 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: AMP.2, MG.3 35 PLIP interactions: 35 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:R.217, A:R.217, A:R.217, A:F.218, A:G.263, A:G.263, A:S.292, A:Q.293, A:G.390, A:E.391, A:E.391, A:Y.451 Salt bridges: A:K.204, A:R.217, A:R.217, A:K.420 pi-Stacking: A:W.421 S0N.19: 30 residues within 4Å: Chain B: K.85, L.191, P.192, H.195, I.196, S.197, S.200, F.218, S.236, 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: AMP.20, MG.21, MG.23 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.196, B:F.218, B:V.238, 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:K.85, B:F.218, B:F.218, B:S.244, B:G.263, B:S.292, B:S.292, B:G.390, B:E.391, B:E.391, B:K.420, B:Y.451 Salt bridges: B:K.204, B:K.420, B:K.450 pi-Stacking: B:W.421, B:W.421

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 19 residues within 4Å: Chain A: T.151, G.263, G.264, P.265, Q.283, S.284, Y.285, G.286, M.287, T.288, E.289, D.366, V.378, R.382, L.385, I.387, N.392 Ligands: S0N.1, MG.9 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.151, A:G.263, A:G.264, A:S.284, A:G.286, A:T.288, A:T.288, A:T.288, A:T.288, A:D.366, A:R.382, A:N.392 Water bridges: A:D.366, A:Y.394, A:Y.394 pi-Stacking: A:Y.285 AMP.20: 17 residues within 4Å: Chain B: T.151, G.263, G.264, P.265, Q.283, S.284, Y.285, G.286, M.287, T.288, E.289, D.366, V.378, L.385, I.387, N.392 Ligands: S0N.19 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.263, B:G.264, B:S.284, B:G.286, B:T.288, B:T.288, B:T.288, B:D.366, B:R.382, B:N.392 Water bridges: B:T.151, B:T.151 pi-Stacking: B:Y.285

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.10, H2O.11, H2O.14 MG.4: 2 residues within 4Å: Chain A: E.350 Ligands: NA.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.350 MG.5: 4 residues within 4Å: Chain A: L.403, H.405, P.406, V.408 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.403, A:H.405, A:V.408, H2O.11 MG.6: 4 residues within 4Å: Chain A: Y.139, M.140, Q.141, F.165 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: D.143, T.164, K.344 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.143, H2O.15, H2O.19 MG.8: 3 residues within 4Å: Chain A: G.339, P.340, V.342 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.339, A:V.342, H2O.15, H2O.16, H2O.18 MG.9: 3 residues within 4Å: Chain A: S.152, Y.394 Ligands: AMP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.394, H2O.3 MG.10: 2 residues within 4Å: Chain A: T.27, E.32 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.27, A:E.32, H2O.15 MG.21: 2 residues within 4Å: Chain B: F.218 Ligands: S0N.19 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.218, H2O.31 MG.22: 1 residues within 4Å: Chain B: H.432 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain B: M.149, H.195, I.196, T.288 Ligands: S0N.19 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.288 MG.24: 3 residues within 4Å: Chain B: L.403, H.405, V.408 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.403, B:H.405, B:V.408, H2O.34

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

NA.11: 2 residues within 4Å: Chain A: E.399, A.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.399 Water bridges: A:R.465, A:R.465, A:R.473 NA.12: 2 residues within 4Å: Chain A: E.350 Ligands: MG.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.348, A:E.350, A:N.353 NA.13: 2 residues within 4Å: Chain A: Q.60, S.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.108, A:S.108 Water bridges: A:Q.60, A:Q.60 NA.14: 2 residues within 4Å: Chain A: E.354, F.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.354 NA.15: 3 residues within 4Å: Chain A: M.9, Q.13 Ligands: PEG.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.13 NA.25: 3 residues within 4Å: Chain B: Y.330, H.332, Y.369 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.332 NA.26: 2 residues within 4Å: Chain B: T.27, E.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.32 NA.27: 3 residues within 4Å: Chain B: K.51, L.75, E.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.51, B:L.75 NA.28: 2 residues within 4Å: Chain B: E.334, G.365 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.334, B:G.365 NA.29: 2 residues within 4Å: Chain B: E.328, P.329 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.329 NA.30: 1 residues within 4Å: Chain B: V.459 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.461, B:D.461 NA.31: 2 residues within 4Å: Chain B: N.228, E.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.228 NA.32: 2 residues within 4Å: Chain B: G.422, K.423 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.423, B:K.423 Water bridges: B:D.418

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

PEG.16: 5 residues within 4Å: Chain A: M.9, A.12, Q.13, F.34 Ligands: NA.15 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain A: G.365, D.366, L.367, R.381 No protein-ligand interaction detected (PLIP) PEG.33: 5 residues within 4Å: Chain A: E.373 Chain B: A.12, Q.13, P.16 Ligands: PEG.34 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:K.311, A:K.311 Hydrogen bonds: B:A.12 PEG.34: 5 residues within 4Å: Chain B: M.9, A.12, Q.13, F.34 Ligands: PEG.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.13

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 5 residues within 4Å: Chain A: H.168, S.171, I.196, S.200, C.291 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.168, A:C.291, H2O.7 CA.35: 5 residues within 4Å: Chain A: P.5 Chain B: S.315, E.317, K.338, G.339 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.315, B:E.317, H2O.31

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
A

B
C

2-succinylbenzoate--CoA ligase

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