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Crystal structure of an archaeal pentameric riboflavin synthase
Analyse Crystal structure of an archaeal pentameric riboflavin synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B98
- Type
- protein
- Length
- 726 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
- Pockets
- 9 · best druggability 0.85
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 | 141 | 56% helix, 18% strand | Q58584 |
| B | Riboflavin synthase (EC 2.5.1.9) | protein | 141 | 55% helix, 18% strand | Q58584 |
| C, E | Riboflavin synthase (EC 2.5.1.9) | protein | 152 | 50% helix, 16% strand | Q58584 |
| D | Riboflavin synthase (EC 2.5.1.9) | protein | 140 | 54% helix, 18% strand | Q58584 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.85 | 0.88 | 111 | empty |
| 2 | 280 | 0.77 | 0.89 | 40 | empty |
| 3 | 228 | 0.69 | 0.86 | 37 | empty |
| 4 | 202 | 0.68 | 0.86 | 32 | empty |
| 5 | 111 | 0.41 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1324 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1322 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1187 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1158 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1149 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 2B98 · PDBe 2B98 · UniProt Q58584
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