SMTL ID : 4j07.1

Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-pentamer

Ligands

5 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: A.91, H.94, T.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.131, A:T.131 NA.3: 3 residues within 4Å: Chain B: A.91, H.94, T.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.94, B:H.94, B:T.131 NA.5: 3 residues within 4Å: Chain C: A.91, H.94, T.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.131 NA.9: 3 residues within 4Å: Chain D: A.91, H.94, T.131 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.94, D:H.94 NA.11: 3 residues within 4Å: Chain E: A.91, H.94, T.131 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.94 Water bridges: E:H.94, E:T.129, E:T.131, E:T.131

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

SO4.2: 4 residues within 4Å: Chain A: G.106, D.107, T.108 Chain B: R.149 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Salt bridges: B:R.149 Hydrogen bonds: A:D.107, A:T.108, A:T.108 Water bridges: A:G.106, A:F.111, A:F.111 SO4.4: 4 residues within 4Å: Chain B: G.106, D.107, T.108 Chain E: R.149 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain B Salt bridges: E:R.149 Hydrogen bonds: B:G.106, B:D.107, B:T.108 Water bridges: B:T.108 SO4.6: 4 residues within 4Å: Chain C: G.106, D.107, T.108 Chain D: R.149 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:R.149, C:T.108 Salt bridges: D:R.149 Hydrogen bonds: C:G.106, C:D.107, C:T.108 SO4.7: 4 residues within 4Å: Chain A: R.149 Chain D: G.106, D.107, T.108 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.107, D:T.108 Water bridges: D:G.106, D:G.106, D:T.108 Salt bridges: A:R.149 SO4.8: 9 residues within 4Å: Chain A: N.116 Chain B: N.116, Q.120 Chain C: N.116, Q.120 Chain D: N.116, Q.120 Chain E: N.116, Q.120 9 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E, 2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:N.116, C:Q.120, E:N.116, E:Q.120, B:N.116, B:Q.120, A:N.116, D:N.116, D:Q.120 SO4.10: 4 residues within 4Å: Chain C: R.149 Chain E: G.106, D.107, T.108 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain E Water bridges: C:R.149, C:K.159, E:G.106, E:T.108, E:T.108 Salt bridges: C:R.149, C:K.159 Hydrogen bonds: E:D.107, E:T.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of a Probable Riboflavin Synthase, Beta chain RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae. TO BE PUBLISHED

Release Date

2013-03-06

Peptides

6,7-dimethyl-8-ribityllumazine synthase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

6,7-dimethyl-8-ribityllumazine synthase