Research workbench
Lumazine synthase from mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl) 1,1 difluoropentane-1- phosphate
Analyse Lumazine synthase from mycobacterium tuberculosis 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
- 2C94
- Type
- protein
- Length
- 730 residues
- Chains
- 5
- 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
- TSF, K
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) | protein | 146 | 50% helix, 21% strand | P66034 |
Ligands and binding sites
- TSF · 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl) 1,1 difluoropentane-1-phosphate · ligand · 5 copies · chains A, B, C, D, E
- K · Potassium ion · metal · 17 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.78 | 0.81 | 57 | empty |
| 2 | 287 | 0.75 | 0.88 | 36 | TSF |
| 3 | 66 | 0.73 | 0.98 | 26 | empty |
| 4 | 270 | 0.73 | 0.86 | 29 | TSF |
| 5 | 271 | 0.72 | 0.86 | 36 | TSF |
Interfaces
5 interfaces between chains.
- A–B · 1195 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1190 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1182 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1167 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1161 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2C94 · LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS 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 2C94 · PDBe 2C94 · UniProt P66034
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