SMTL ID : 4els.1

Structure of E. Coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex with bicarbonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

9 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.1: 9 residues within 4Å: Chain A: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.154, A:T.155, A:S.161 Water bridges: A:S.161 BCT.6: 9 residues within 4Å: Chain B: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.154, B:S.161 Water bridges: B:G.133, B:D.163 BCT.7: 4 residues within 4Å: Chain B: T.203, E.213, W.217 Chain E: R.188 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:E.213, B:W.217, E:R.188 BCT.10: 9 residues within 4Å: Chain C: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.155 BCT.14: 9 residues within 4Å: Chain D: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.156 Water bridges: D:T.155, D:D.163 BCT.15: 5 residues within 4Å: Chain A: R.188 Chain D: T.203, V.205, E.213, W.217 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.188, D:E.213 BCT.17: 7 residues within 4Å: Chain E: G.132, G.133, Q.154, T.155, G.156, S.161, W.184 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.155 BCT.18: 5 residues within 4Å: Chain E: T.203, V.205, E.213, W.217 Chain F: R.188 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.188, F:R.188, E:T.203 Water bridges: E:T.203 BCT.19: 9 residues within 4Å: Chain F: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.132, F:Q.154, F:T.155, F:T.155, F:G.156

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.203, V.205, E.213, R.216, W.217 Chain C: R.188 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.188, C:R.188, A:T.203, A:R.216 GOL.9: 7 residues within 4Å: Chain B: S.19, F.22, E.23, D.24, I.25, R.26, N.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.19, B:S.19, B:I.25, B:N.40 GOL.11: 7 residues within 4Å: Chain C: Y.10, T.203, V.205, E.213, R.216, W.217 Chain D: R.188 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.10, C:T.203, C:E.213, C:R.216, D:R.188, D:R.188 GOL.20: 7 residues within 4Å: Chain B: R.188 Chain F: Y.10, T.203, V.205, E.213, R.216, W.217 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:Y.10, F:T.203, F:E.213, F:R.216, B:R.188, B:R.188

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: I.174, V.175 Chain C: G.176 Chain D: I.174, V.175 Ligands: CL.4 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: R.173, D.239, C.240 Chain D: A.238, D.239 Chain F: G.242 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.173, D:A.238 Water bridges: A:D.239, A:C.240 EDO.22: 3 residues within 4Å: Chain A: Y.258 Chain F: G.86, S.161 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.161, F:S.161

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

CL.4: 1 residues within 4Å: Ligands: EDO.3 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: P.50, L.51 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: R.49, L.51 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain C: E.23 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: R.173, D.239, C.240 Ligand excluded by PLIP

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

PEG.21: 4 residues within 4Å: Chain B: R.173 Chain E: R.173 Chain F: A.172, R.173 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Y.R. et al., Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways. Biochemistry (2012)

Release Date

2012-06-06

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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