Research workbench
Complex structure of bacillus subtilis ribg reduction mechanism in riboflavin biosynthesis
Analyse Complex structure of bacillus subtilis ribg reduction mechanism in riboflavin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EX8
- Type
- protein
- Length
- 1,437 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribd
- EC
- 3.5.4.26, 1.1.1.193
- UniProt
- P17618
- Ligands
- AIF, ZN
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 359 | 30% helix, 24% strand | P17618 |
| D | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 360 | 29% helix, 24% strand | P17618 |
Ligands and binding sites
- AIF · [(2R,3S,4R,5E)-5-[(5-amino-2,6-dioxo-3H-pyrimidin-4-yl)imino]-2,3,4-trihydroxy-pentyl] dihydrogen phosphate · ligand · chains C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.74 | 0.81 | 50 | empty |
| 2 | 590 | 0.73 | 0.81 | 52 | empty |
| 3 | 525 | 0.70 | 0.79 | 53 | empty |
| 4 | 502 | 0.69 | 0.80 | 52 | empty |
| 5 | 307 | 0.65 | 0.81 | 34 | AIF |
Interfaces
4 interfaces between chains.
- B–D · 2047 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2034 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1113 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1015 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3EX8 · Complex structure of bacillus subtilis RibG reduction mechanism in riboflavin biosynthesis · the same entry in another collection · chain A against A, TM-score 1.00
- P17618 · AlphaFold monomer V2.0 prediction for riboflavin biosynthesis protein ribd (P17618) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P17618
- Elsewhere: RCSB PDB 3EX8 · PDBe 3EX8 · UniProt P17618
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