MolNFT v1 · #20969 · protein
SYNTHASE/RIBOFLAVIN synthase complex of bacillus subtilis
1RVV: “SYNTHASE/RIBOFLAVIN synthase complex of bacillus subtilis”. X-ray diffraction, 2 ligands (INI, PO4), 20 pockets (best druggability 0.87). MolNFT v1 #20969 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RVV
- Type
- protein
- Length
- 4,620 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin synthase
- UniProt
- P11998
- Ligands
- INI, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4 | Riboflavin synthase | protein | 154 | 50% helix, 24% strand | P11998 |
Ligands and binding sites
- INI · 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 30 copies · chains A, E, B, C, D, F, J, G, H, I, K, O, L, M, N, P, T, Q, R, S, U, Y, V, W, X, Z, 4, 1, 2, 3
- PO4 · Phosphate ion · ion · 30 copies · chains A, E, B, C, D, F, J, G, H, I, K, O, L, M, N, P, T, Q, R, S, U, Y, V, W, X, Z, 4, 1, 2, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.87 | 0.88 | 93 | PO4, INI |
| 2 | 1053 | 0.87 | 0.88 | 101 | PO4, INI |
| 3 | 1044 | 0.86 | 0.87 | 94 | PO4, INI |
| 4 | 1076 | 0.86 | 0.87 | 101 | PO4, INI |
| 5 | 978 | 0.86 | 0.88 | 99 | PO4, INI |
Interfaces
87 interfaces between chains.
- X–Y · 1446 Ų buried · 20 hydrogen bonds · protein-protein
- M–N · 1443 Ų buried · 21 hydrogen bonds · protein-protein
- Z–4 · 1443 Ų buried · 21 hydrogen bonds · protein-protein
- K–O · 1442 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1441 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1RVV · SYNTHASE/RIBOFLAVIN synthase complex of bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
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 P11998
- Elsewhere: RCSB PDB 1RVV · PDBe 1RVV · UniProt P11998
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