Research workbench
Lumazine synthase from mycobacterium tuberculosis bound to 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-YL)BUTYL phosphate
Analyse Lumazine synthase from mycobacterium tuberculosis bound to 4-(6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C97
- Type
- protein
- Length
- 733 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
- JCL, K
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) | protein | 147 | 49% helix, 19% strand | P66034 |
| C, E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) | protein | 146 | 50% helix, 21% strand | P66034 |
Ligands and binding sites
- JCL · 4-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl) butyl phosphate · ligand · 5 copies · chains A, B, C, D, E
- K · Potassium ion · metal · 16 copies · chains A, B, C, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, E, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D, E
- DTD · Dithiane diol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.78 | 0.97 | 30 | MPD |
| 2 | 111 | 0.78 | 0.97 | 31 | MPD |
| 3 | 100 | 0.78 | 0.98 | 29 | MPD |
| 4 | 792 | 0.78 | 0.82 | 53 | MPD |
| 5 | 107 | 0.77 | 0.97 | 29 | MPD |
Interfaces
5 interfaces between chains.
- B–C · 1196 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1195 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 1176 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1166 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 2C97 · LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6… · 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 2C97 · PDBe 2C97 · UniProt P66034
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