SMTL ID : 2b99.1

Crystal Structure of an archaeal pentameric riboflavin synthase Complex with a Substrate analog inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-pentamer

Ligands

10 x RDL: 6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE(Non-covalent)

RDL.1: 15 residues within 4Å: Chain A: F.12, P.40, G.41, I.42, K.43, D.44, M.66, P.67, G.68, D.73, C.76 Chain B: I.96, E.97, H.122 Ligands: RDL.3 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.42, A:K.43, A:K.43, A:D.44, A:M.66, A:G.68, A:D.73, B:E.97 Water bridges: A:M.66 pi-Stacking: A:F.12 RDL.2: 9 residues within 4Å: Chain A: F.99, E.104, R.118, H.122, R.145 Chain E: F.12, G.68, D.73 Ligands: RDL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.104, A:R.118, A:R.118, A:H.122 pi-Cation interactions: A:R.118 RDL.3: 6 residues within 4Å: Chain A: D.73 Chain B: F.99, E.104, R.118, H.122 Ligands: RDL.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.99, B:R.118, B:R.118 pi-Cation interactions: B:R.118 RDL.4: 8 residues within 4Å: Chain B: F.12, K.72, D.73 Chain D: F.99, E.104, R.118, H.122 Ligands: RDL.5 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:F.99, D:R.118, D:H.122, B:D.73 pi-Cation interactions: D:R.118 RDL.5: 15 residues within 4Å: Chain B: F.12, P.40, G.41, I.42, K.43, D.44, M.66, P.67, G.68, D.73, C.76 Chain D: I.96, E.97, H.122 Ligands: RDL.4 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.41, B:I.42, B:K.43, B:K.43, B:D.44, B:M.66, B:G.68, B:D.73, B:D.73, D:E.97, D:E.97 Water bridges: B:T.10, B:M.66 pi-Stacking: B:F.12 RDL.6: 15 residues within 4Å: Chain C: F.12, P.40, G.41, I.42, K.43, D.44, M.66, P.67, G.68, D.73, C.76 Chain E: I.96, E.97, H.122 Ligands: RDL.9 13 PLIP interactions: 3 interactions with chain E, 10 interactions with chain C Hydrogen bonds: E:I.95, E:E.97, E:E.97, C:G.41, C:I.42, C:K.43, C:K.43, C:D.44, C:M.66, C:G.68, C:D.73 Water bridges: C:T.10 pi-Stacking: C:F.12 RDL.7: 11 residues within 4Å: Chain C: E.97, F.99, H.101, E.104, R.118, H.122, R.145, Q.146 Chain D: F.12, D.73 Ligands: RDL.8 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:H.101, C:R.118, C:R.118, C:Q.146, C:Q.146, D:D.73 Water bridges: C:F.99, C:F.99, C:Q.146, D:A.70 pi-Cation interactions: C:R.118 RDL.8: 16 residues within 4Å: Chain C: I.96, E.97, H.122, Q.146 Chain D: F.12, P.40, G.41, I.42, K.43, D.44, M.66, P.67, G.68, D.73, C.76 Ligands: RDL.7 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:P.40, D:I.42, D:K.43, D:M.66, D:G.68, D:D.73, C:E.97 Water bridges: D:T.10 pi-Stacking: D:F.12 RDL.9: 11 residues within 4Å: Chain C: F.12, K.72, D.73 Chain E: F.99, H.101, E.104, R.118, H.122, R.145, Q.146 Ligands: RDL.6 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:H.101, E:R.118, E:R.118, E:R.145, E:Q.146, E:Q.146, C:D.73 Water bridges: E:R.145, C:E.102 pi-Cation interactions: E:R.118 RDL.10: 15 residues within 4Å: Chain A: I.96, E.97, H.122 Chain E: F.12, P.40, G.41, I.42, K.43, D.44, M.66, P.67, G.68, D.73, C.76 Ligands: RDL.2 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:G.41, E:I.42, E:K.43, E:K.43, E:D.44, E:M.66, E:G.68, E:D.73, A:E.97, A:E.97 pi-Stacking: E:F.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramsperger, A. et al., Crystal Structure of an Archaeal Pentameric Riboflavin Synthase in Complex with a Substrate Analog Inhibitor: stereochemical implications. J.Biol.Chem. (2006)

Release Date

2005-11-08

Peptides

Riboflavin synthase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Riboflavin synthase

Related Entries With Identical Sequence