Research workbench
Lumazine synthase from mycobacterium tuberculosus bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)
Analyse Lumazine synthase from mycobacterium tuberculosus bound to 3-(1,3,7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C9B
- Type
- protein
- Length
- 1,466 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase
- EC
- 2.5.1.9
- UniProt
- P66034
- Ligands
- PUG, K, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, G, I | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) | protein | 147 | 49% helix, 20% strand | P66034 |
| C, E, H, J | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) | protein | 146 | 50% helix, 21% strand | P66034 |
Ligands and binding sites
- PUG · 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl) · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- K · Potassium ion · metal · 15 copies · chains A, H, B, C, F, D, J, E, I, G
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.83 | 0.85 | 93 | K |
| 2 | 343 | 0.79 | 0.89 | 51 | PUG, PO4 |
| 3 | 318 | 0.79 | 0.90 | 50 | PUG, PO4 |
| 4 | 886 | 0.79 | 0.81 | 55 | MPD |
| 5 | 357 | 0.78 | 0.88 | 48 | PUG, PO4 |
Interfaces
25 interfaces between chains.
- F–J · 1195 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1175 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1174 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1173 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1165 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2C9B · Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7… · 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 P66034
- Elsewhere: RCSB PDB 2C9B · PDBe 2C9B · UniProt P66034
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