SMTL ID : 3t88.1

Crystal structure of Escherichia coli MenB in complex with substrate analogue, OSB-NCoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

S0N.1: 30 residues within 4Å: Chain A: Q.47, V.48, R.49, A.51, F.52, S.88, G.89, G.90, D.91, Q.92, K.93, Y.101, L.110, V.112, L.113, Y.133, I.135, G.136, G.137, T.159, V.163, S.165, F.166, D.167, Q.193 Chain E: T.258, Y.262, F.274, K.277 Ligands: CL.2 26 PLIP interactions: 21 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:L.110, A:V.112, A:L.113, A:I.135, A:D.167, E:T.258 Hydrogen bonds: A:S.88, A:S.88, A:G.90, A:G.90, A:D.91, A:Q.92, A:K.93, A:G.137, A:T.159, A:S.165, A:S.165 Water bridges: A:K.93, A:D.167, E:K.277 Salt bridges: A:R.49, A:R.49, A:K.93, E:K.277 pi-Stacking: E:F.274, E:F.274 S0N.5: 30 residues within 4Å: Chain B: Q.47, V.48, R.49, A.51, F.52, S.88, G.89, G.90, D.91, Q.92, K.93, Y.101, L.110, V.112, L.113, Y.133, I.135, G.136, G.137, T.159, V.163, S.165, F.166, D.167, Q.193 Chain F: T.258, Y.262, F.274, K.277 Ligands: CL.6 29 PLIP interactions: 8 interactions with chain F, 21 interactions with chain B Hydrophobic interactions: F:T.258, B:L.110, B:V.112, B:L.113, B:Y.133, B:I.135, B:D.167 Hydrogen bonds: F:Y.262, F:Y.262, F:K.277, B:S.88, B:S.88, B:G.90, B:G.90, B:Q.92, B:K.93, B:G.137, B:T.159, B:S.165, B:S.165, B:F.166 Water bridges: F:K.277, B:K.93 Salt bridges: F:K.277, B:R.49, B:R.49, B:K.93 pi-Stacking: F:F.274, F:F.274 S0N.9: 29 residues within 4Å: Chain C: Q.47, V.48, R.49, A.51, F.52, S.88, G.89, G.90, D.91, Q.92, K.93, Y.101, L.110, V.112, L.113, Y.133, I.135, G.137, T.159, V.163, S.165, F.166, D.167, Q.193 Chain D: T.258, Y.262, F.274, K.277 Ligands: CL.10 32 PLIP interactions: 24 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:L.110, C:V.112, C:L.113, C:Y.133, C:I.135, C:D.167, D:T.258 Hydrogen bonds: C:S.88, C:S.88, C:G.90, C:G.90, C:D.91, C:Q.92, C:K.93, C:Y.133, C:Y.133, C:G.137, C:T.159, C:S.165, C:S.165, C:F.166, D:Y.262, D:Y.262, D:K.277 Water bridges: C:K.93, D:K.277 Salt bridges: C:R.49, C:R.49, C:K.93, D:K.277 pi-Stacking: D:F.274, D:F.274 S0N.13: 29 residues within 4Å: Chain C: T.258, Y.262, F.274 Chain D: Q.47, V.48, R.49, A.51, F.52, S.88, G.89, G.90, D.91, Q.92, K.93, Y.101, L.110, V.112, L.113, Y.133, I.135, G.136, G.137, T.159, V.163, S.165, F.166, D.167, Q.193 Ligands: CL.14 27 PLIP interactions: 23 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.110, D:V.112, D:L.113, D:Y.133, D:I.135, D:D.167, C:T.258 Hydrogen bonds: D:S.88, D:S.88, D:G.90, D:G.90, D:D.91, D:Q.92, D:K.93, D:Y.101, D:Y.133, D:Y.133, D:G.137, D:S.165, D:S.165, D:F.166, C:Y.262 Salt bridges: D:R.49, D:R.49, D:K.93 pi-Stacking: C:F.274, C:F.274 S0N.17: 30 residues within 4Å: Chain A: T.258, Y.262, F.274, K.277 Chain E: Q.47, V.48, R.49, A.51, F.52, S.88, G.89, G.90, D.91, Q.92, K.93, Y.101, L.110, V.112, L.113, Y.133, I.135, G.136, G.137, T.159, V.163, S.165, F.166, D.167, Q.193 Ligands: CL.18 28 PLIP interactions: 23 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:L.110, E:V.112, E:L.113, E:Y.133, E:Y.133, E:I.135, E:D.167, A:T.258 Hydrogen bonds: E:S.88, E:S.88, E:G.90, E:G.90, E:Q.92, E:K.93, E:Y.101, E:Y.133, E:G.137, E:S.165, E:S.165, A:K.277 Water bridges: E:K.93, E:D.167 Salt bridges: E:R.49, E:R.49, E:K.93, A:K.277 pi-Stacking: A:F.274, A:F.274 S0N.21: 30 residues within 4Å: Chain B: T.258, Y.262, F.274, K.277 Chain F: Q.47, V.48, R.49, A.51, F.52, S.88, G.89, G.90, D.91, Q.92, K.93, Y.101, L.110, V.112, L.113, Y.133, I.135, G.136, G.137, T.159, V.163, S.165, F.166, D.167, Q.193 Ligands: CL.22 28 PLIP interactions: 22 interactions with chain F, 6 interactions with chain B Hydrophobic interactions: F:L.110, F:V.112, F:L.113, F:Y.133, F:I.135, F:D.167, B:T.258 Hydrogen bonds: F:S.88, F:S.88, F:G.90, F:G.90, F:D.91, F:Q.92, F:K.93, F:Y.101, F:G.137, F:S.165, F:S.165, B:Y.262, B:K.277 Water bridges: F:K.93, F:D.167 Salt bridges: F:R.49, F:R.49, F:K.93, B:K.277 pi-Stacking: B:F.274, B:F.274

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

CL.2: 6 residues within 4Å: Chain A: G.136, Q.158, T.159, G.160, W.188 Ligands: S0N.1 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain B: G.136, Q.158, T.159, G.160, W.188 Ligands: S0N.5 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain C: G.136, Q.158, T.159, G.160, W.188 Ligands: S0N.9 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain D: G.136, Q.158, T.159, G.160, W.188 Ligands: S0N.13 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain E: G.136, Q.158, T.159, G.160, W.188 Ligands: S0N.17 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain F: G.136, Q.158, T.159, G.160, W.188 Ligands: S0N.21 Ligand excluded by PLIP

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: P.54, K.58, D.103, H.109 Chain E: Y.69 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.111 PGE.7: 7 residues within 4Å: Chain B: P.54, L.55, K.58, D.103, H.109, N.111 Chain F: Y.69 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.111 PGE.11: 5 residues within 4Å: Chain C: L.55, K.58, D.103, H.109 Chain D: Y.69 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.58, C:D.103 Water bridges: C:N.111 PGE.15: 7 residues within 4Å: Chain C: Y.69 Chain D: P.54, L.55, K.58, D.103, H.109, N.111 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.58 Water bridges: D:N.111 PGE.19: 6 residues within 4Å: Chain A: Y.69 Chain E: P.54, L.55, K.58, H.109, N.111 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.58 Water bridges: E:D.104, E:N.111 PGE.23: 6 residues within 4Å: Chain B: Y.69 Chain F: P.54, K.58, D.103, H.109, N.111 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.58 Water bridges: F:N.111

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Y.14, T.207, V.209, E.217, R.220, W.221 Chain C: R.192 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.14, A:T.207, A:T.207, A:E.217, C:R.192, C:R.192 GOL.8: 7 residues within 4Å: Chain A: R.192 Chain B: Y.14, T.207, V.209, E.217, R.220, W.221 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.192, A:R.192, B:R.220 GOL.12: 7 residues within 4Å: Chain B: R.192 Chain C: Y.14, T.207, V.209, E.217, R.220, W.221 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.207, C:E.217, C:R.220, B:R.192, B:R.192 GOL.16: 6 residues within 4Å: Chain D: T.207, V.209, E.217, R.220, W.221 Chain E: R.192 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:R.192, E:R.192, D:Y.14, D:T.207, D:T.207, D:R.220 Water bridges: D:V.208 GOL.20: 7 residues within 4Å: Chain E: Y.14, T.207, V.209, E.217, R.220, W.221 Chain F: R.192 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.192, F:R.192, E:Y.14, E:R.220, E:R.220 GOL.24: 7 residues within 4Å: Chain D: R.192 Chain F: Y.14, T.207, V.209, E.217, R.220, W.221 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.192, D:R.192, F:R.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H.J. et al., Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member. Biochemistry (2011)

Release Date

2011-08-24

Peptides

1,4-Dihydroxy-2-naphthoyl-CoA synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

1,4-Dihydroxy-2-naphthoyl-CoA synthase

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