SMTL ID : 3t89.1

Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

6 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 9 residues within 4Å: Chain A: G.136, G.137, Q.158, T.159, G.160, S.165, F.166, D.167, W.188 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.158, A:T.159, A:G.160, A:S.165 Water bridges: A:G.137 MLI.4: 9 residues within 4Å: Chain B: G.136, G.137, Q.158, T.159, G.160, S.165, F.166, D.167, W.188 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.188 Hydrogen bonds: B:Q.158, B:T.159, B:T.159, B:G.160 Water bridges: B:G.137 MLI.7: 9 residues within 4Å: Chain C: G.136, G.137, Q.158, T.159, G.160, S.165, F.166, D.167, W.188 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.158, C:T.159, C:G.160, C:S.165 Water bridges: C:G.137 MLI.9: 9 residues within 4Å: Chain D: G.136, G.137, Q.158, T.159, G.160, S.165, F.166, D.167, W.188 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.158, D:T.159, D:T.159, D:G.160, D:S.165 Water bridges: D:G.137 MLI.12: 9 residues within 4Å: Chain E: G.136, G.137, Q.158, T.159, G.160, S.165, F.166, D.167, W.188 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.188 Hydrogen bonds: E:G.137, E:Q.158, E:T.159, E:G.160 MLI.14: 9 residues within 4Å: Chain F: G.136, G.137, Q.158, T.159, G.160, S.165, F.166, D.167, W.188 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.158, F:T.159, F:T.159, F:G.160 Water bridges: F:G.137

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Y.14, T.207, V.209, E.217, R.220, W.221 Chain C: R.192 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.207, A:R.220, C:R.192, C:R.192 GOL.3: 9 residues within 4Å: Chain A: I.178, V.179, G.180 Chain C: A.176, I.178, V.179, G.180 Chain D: I.178, G.180 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C Water bridges: A:A.176, A:R.177, D:R.177, C:A.176 GOL.5: 6 residues within 4Å: Chain B: T.207, V.209, E.217, R.220, W.221 Chain E: R.192 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:R.220, E:R.192, E:R.192 GOL.6: 6 residues within 4Å: Chain B: S.23, F.26, E.27, D.28, I.29, N.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.44, B:N.44 GOL.8: 7 residues within 4Å: Chain C: Y.14, T.207, V.209, E.217, R.220, W.221 Chain D: R.192 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.192, D:R.192, C:Y.14, C:T.207, C:E.217, C:R.220 GOL.10: 6 residues within 4Å: Chain A: R.192 Chain D: T.207, V.209, E.217, R.220, W.221 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.192, A:R.192, D:R.220 GOL.11: 8 residues within 4Å: Chain B: R.177, I.178 Chain E: A.176, V.179, G.180 Chain F: I.178, V.179, G.180 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.176, E:V.179 GOL.13: 7 residues within 4Å: Chain E: Y.14, T.207, V.209, E.217, R.220, W.221 Chain F: R.192 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.207, E:E.217, E:R.220, E:R.220, F:R.192, F:R.192 Water bridges: E:T.207 GOL.15: 7 residues within 4Å: Chain B: R.192 Chain F: Y.14, T.207, V.209, E.217, R.220, W.221 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:Y.14, F:R.220, F:R.220, B:R.192, B:R.192

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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