Research workbench
Crystal structure of an archaeal pentameric riboflavin synthase complex with a substrate analog inhibitor
Analyse Crystal structure of an archaeal pentameric riboflavin synthase complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B99
- Type
- protein
- Length
- 734 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin synthase
- EC
- 2.5.1.9
- UniProt
- Q58584
- Ligands
- RDL
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin synthase (EC 2.5.1.9) | protein | 146 | 54% helix, 17% strand | Q58584 |
| B | Riboflavin synthase (EC 2.5.1.9) | protein | 143 | 55% helix, 17% strand | Q58584 |
| C, E | Riboflavin synthase (EC 2.5.1.9) | protein | 152 | 52% helix, 16% strand | Q58584 |
| D | Riboflavin synthase (EC 2.5.1.9) | protein | 141 | 55% helix, 18% strand | Q58584 |
Ligands and binding sites
- RDL · 6,7-dioxo-5H-8-ribitylaminolumazine · ligand · 10 copies · chains A, B, E, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.82 | 0.85 | 84 | RDL |
| 2 | 385 | 0.78 | 0.87 | 40 | RDL |
| 3 | 355 | 0.77 | 0.88 | 40 | RDL |
| 4 | 515 | 0.76 | 0.84 | 47 | RDL |
| 5 | 335 | 0.72 | 0.84 | 35 | RDL |
Interfaces
5 interfaces between chains.
- C–E · 1311 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1299 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1263 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1244 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1158 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2B99 · Crystal Structure of an archaeal pentameric riboflavin synthase Complex with a Substrate… · the same entry in another collection · chain E against E, TM-score 1.00
- Q58584 · AlphaFold monomer V2.0 prediction for riboflavin synthase (Q58584) · a predicted model of the same protein · chain A 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 Q58584
- Elsewhere: RCSB PDB 2B99 · PDBe 2B99 · UniProt Q58584
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