SMTL ID : 4elx.1

Structure of apo E.coli. 1,4-dihydroxy-2- naphthoyl CoA synthases with Cl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-hexamer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.10, T.203, V.205, E.213, R.216, W.217 Chain C: R.188 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.203, A:R.216, C:R.188, C:R.188 GOL.3: 6 residues within 4Å: Chain B: Y.10, V.205, E.213, R.216, W.217 Chain E: R.188 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:E.213, B:E.213, E:R.188, E:R.188 Water bridges: B:T.203, B:T.203 GOL.7: 7 residues within 4Å: Chain C: Y.10, T.203, V.205, E.213, R.216, W.217 Chain D: R.188 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.10, C:T.203, C:E.213, C:R.216, C:W.217, D:R.188, D:R.188 GOL.11: 7 residues within 4Å: Chain A: R.188 Chain D: Y.10, T.203, V.205, E.213, R.216, W.217 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.188, A:R.188, D:R.216 GOL.14: 7 residues within 4Å: Chain E: Y.10, T.203, V.205, E.213, R.216, W.217 Chain F: R.188 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.203, E:R.216, E:R.216, F:R.188, F:R.188 Water bridges: E:T.203 GOL.16: 6 residues within 4Å: Chain B: R.188 Chain F: T.203, V.205, E.213, R.216, W.217 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:Y.10, F:T.203, F:R.216, B:R.188, B:R.188 Water bridges: F:N.202, B:E.182, B:R.188 GOL.19: 6 residues within 4Å: Chain F: T.75, G.76, G.78, D.79, M.125, L.210 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.75, F:D.79 Water bridges: F:A.127, F:L.210

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

CL.2: 5 residues within 4Å: Chain A: G.132, Q.154, T.155, G.156, W.184 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain B: G.132, Q.154, T.155, G.156, W.184 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: G.132, Q.154, T.155, G.156, W.184 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain D: G.132, Q.154, T.155, G.156, W.184 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain F: G.132, Q.154, T.155, G.156, W.184 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain F: R.173, D.239 Ligand excluded by PLIP

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

PEG.5: 12 residues within 4Å: Chain B: R.173, I.174, V.175, G.176 Chain E: A.172, I.174, G.176 Chain F: A.172, R.173, I.174, V.175, G.176 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:I.174, E:A.172 PEG.9: 13 residues within 4Å: Chain A: A.172, R.173, I.174, V.175, G.176 Chain C: A.172, R.173, G.176 Chain D: A.172, R.173, I.174, V.175, G.176 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.173, C:G.176, D:V.175 PEG.13: 8 residues within 4Å: Chain B: G.242, Q.243, L.246 Chain C: A.238, D.239 Chain D: R.173, D.239, C.240 11 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:D.239, D:R.173, D:R.173, D:D.239, B:Q.243 Water bridges: C:R.173, C:R.173, C:A.238, C:A.238, C:D.239, C:G.242

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

EDO.6: 2 residues within 4Å: Chain B: Y.65 Chain D: L.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.106, D:L.106 EDO.15: 8 residues within 4Å: Chain C: Q.247, A.250 Chain E: G.165, W.166, G.167, A.168, S.169, Y.170 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.167, E:G.167, E:Y.170, C:L.246, C:Q.247 Water bridges: E:S.169

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 6 residues within 4Å: Chain C: T.75, G.76, G.78, D.79, M.125, E.211 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.75, C:G.78, C:G.78, C:D.79 Water bridges: C:A.127, C:E.211

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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