Research workbench
Crystal structure of a probable riboflavin synthase, beta chain ribh (6,7-dimethyl-8-ribityllumazine synthase, dmrl synthase, lumazine synthase) from mycobacterium leprae
Analyse Crystal structure of a probable riboflavin synthase, beta chain ribh… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J07
- Type
- protein
- Length
- 743 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase
- EC
- 2.5.1.78
- UniProt
- B8ZUN3
- Ligands
- NA, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 152 | 49% helix, 18% strand | B8ZUN3 |
| B | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 148 | 51% helix, 19% strand | B8ZUN3 |
| C | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 149 | 50% helix, 20% strand | B8ZUN3 |
| D | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 146 | 51% helix, 19% strand | B8ZUN3 |
| E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 148 | 50% helix, 20% strand | B8ZUN3 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.80 | 0.82 | 53 | SO4 |
| 2 | 296 | 0.71 | 0.85 | 30 | SO4 |
| 3 | 281 | 0.70 | 0.84 | 29 | SO4 |
| 4 | 248 | 0.70 | 0.85 | 30 | SO4 |
| 5 | 308 | 0.68 | 0.83 | 32 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1192 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1178 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1153 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1148 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1130 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4J07 · Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH… · the same entry in another collection · chain E against E, TM-score 1.00
- B8ZUN3 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (B8ZUN3) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B8ZUN3
- Elsewhere: RCSB PDB 4J07 · PDBe 4J07 · UniProt B8ZUN3
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