SMTL ID : 4eml.1

Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with bicarbonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-hexamer

Ligands

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

BCT.1: 7 residues within 4Å: Chain A: G.122, G.123, Q.144, T.145, G.146, F.152, W.174 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.122, A:Q.144, A:T.145, A:G.146 Water bridges: A:T.145 BCT.5: 7 residues within 4Å: Chain B: G.122, G.123, Q.144, T.145, G.146, F.152, W.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.144, B:T.145 Water bridges: B:G.123 BCT.8: 7 residues within 4Å: Chain C: G.122, G.123, Q.144, T.145, G.146, W.174 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.122, C:Q.144, C:T.145, C:G.146 Water bridges: C:T.145 BCT.12: 7 residues within 4Å: Chain D: G.122, G.123, Q.144, T.145, G.146, F.152, W.174 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.144, D:S.151 Water bridges: D:D.153 BCT.14: 7 residues within 4Å: Chain E: G.122, G.123, Q.144, T.145, G.146, F.152, W.174 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.122, E:Q.144, E:T.145, E:G.146 BCT.18: 7 residues within 4Å: Chain F: G.122, G.123, Q.144, T.145, G.146, F.152, W.174 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.122, F:Q.144, F:T.145, F:G.146

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 8 residues within 4Å: Chain A: T.61, G.62, G.64, Y.71, L.115, V.197, L.200, E.201 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.61, A:L.115 Water bridges: A:L.200 MPD.15: 7 residues within 4Å: Chain E: T.61, G.62, Y.71, L.115, V.197, L.200, E.201 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.71, E:L.115, E:V.197, E:L.200, E:E.201 Water bridges: E:G.64, E:G.64, E:G.64, E:G.64 MPD.19: 7 residues within 4Å: Chain F: T.61, G.62, G.64, Y.71, L.115, L.200, E.201 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:T.61, F:Y.71, F:L.115, F:L.200, F:E.201 Hydrogen bonds: F:G.64 Water bridges: F:G.64

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

CL.3: 5 residues within 4Å: Chain A: D.198, R.199, L.200, E.201, E.202 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: K.169, E.172 Chain D: N.192 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain E: A.162 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain B: T.61, G.62, G.64, L.115, L.200, E.201 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.61, B:G.62, B:G.64 GOL.7: 7 residues within 4Å: Chain B: S.269, Q.270, Y.271, P.272, W.273 Chain C: N.53, R.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.273 Water bridges: B:S.269, B:Y.271 GOL.9: 8 residues within 4Å: Chain C: V.98, S.151, F.152, D.153 Chain E: T.244, Y.248 Ligands: BCT.8, SO4.10 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:Y.248, E:Y.248, C:D.153 Water bridges: C:G.123, C:D.153, C:G.154 GOL.11: 5 residues within 4Å: Chain C: T.61, G.64, L.115, L.200, E.201 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.61, C:G.64, C:E.201 GOL.13: 5 residues within 4Å: Chain D: T.61, G.62, A.63, G.64, E.201 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.61, D:G.64, D:G.64 Water bridges: D:E.201 GOL.17: 5 residues within 4Å: Chain A: N.53 Chain E: S.269, Q.270, Y.271, P.272 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E Water bridges: A:R.54, E:S.269, E:Y.271 Hydrogen bonds: E:S.269 GOL.20: 4 residues within 4Å: Chain F: I.141, Q.179, Y.180, S.181 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.179, F:Y.180 Water bridges: F:S.181

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain C: N.97 Chain E: G.241, Y.248 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.97, C:N.97

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

2012-06-20

Peptides

Naphthoate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Naphthoate synthase

Related Entries With Identical Sequence