SMTL ID : 4elw.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

8 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 9 residues within 4Å: Chain A: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.154, A:T.155, A:G.156, A:D.163 Water bridges: A:D.163 NO3.4: 9 residues within 4Å: Chain B: G.132, G.133, Q.154, T.155, G.156, S.161, F.162, D.163, W.184 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.132, B:Q.154, B:T.155, B:G.156, B:D.163 Water bridges: B:S.161, B:S.161, B:D.163 NO3.5: 7 residues within 4Å: Chain B: Y.10, T.203, V.205, E.213, R.216, W.217 Chain E: R.188 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:R.188, E:R.188, B:E.213 NO3.8: 6 residues within 4Å: Chain C: G.132, Q.154, T.155, G.156, D.163, W.184 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.154, C:T.155, C:G.156 Water bridges: C:G.133 NO3.10: 9 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:Q.154, D:T.155, D:T.155, D:G.156, D:D.163 NO3.12: 9 residues within 4Å: Chain E: 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 E Hydrogen bonds: E:G.132, E:Q.154, E:T.155, E:G.156 NO3.13: 5 residues within 4Å: Chain E: T.203, V.205, E.213, W.217 Chain F: R.188 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.203, E:E.213, E:E.213, F:R.188, F:R.188 NO3.14: 8 residues within 4Å: Chain F: G.132, G.133, Q.154, T.155, G.156, F.162, D.163, W.184 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.132, F:Q.154, F:T.155, F:G.156

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 11 residues within 4Å: Chain A: A.172, R.173, I.174, V.175, G.176 Chain C: R.173, I.174 Chain D: A.172, R.173, V.175, G.176 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:V.175, A:A.172 SIN.7: 12 residues within 4Å: Chain B: A.172, R.173, I.174, V.175 Chain E: A.172, R.173, I.174, G.176 Chain F: A.172, R.173, V.175, G.176 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:R.173, B:I.174

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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 A, 2 interactions with chain C Hydrogen bonds: A:T.203, A:R.216, C:R.188, C:R.188 GOL.9: 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:Y.10, C:T.203, C:E.213, C:W.217, D:R.188, D:R.188 GOL.11: 6 residues within 4Å: Chain A: R.188 Chain D: 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.15: 7 residues within 4Å: Chain B: R.188 Chain F: Y.10, T.203, V.205, E.213, R.216, W.217 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:R.188, B:R.188, F:Y.10, F:T.203, F:R.216

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

CL.6: 1 residues within 4Å: Chain B: L.51 Ligand excluded by 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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