Research workbench
Crystal structure of 6-phosphogluconolactonase from mycobacterium tuberculosis
Analyse Crystal structure of 6-phosphogluconolactonase from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ICO
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconolactonase
- EC
- 3.1.1.31
- UniProt
- P63338
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-phosphogluconolactonase (EC 3.1.1.31) | protein | 244 | 40% helix, 19% strand | P63338 |
| C, D | 6-phosphogluconolactonase (EC 3.1.1.31) | protein | 247 | 38% helix, 19% strand | P63338 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.67 | 0.81 | 58 | SO4 |
| 2 | 584 | 0.66 | 0.77 | 49 | empty |
| 3 | 244 | 0.53 | 0.76 | 24 | empty |
| 4 | 106 | 0.50 | 0.82 | 23 | SO4 |
| 5 | 118 | 0.50 | 0.81 | 23 | SO4 |
Interfaces
5 interfaces between chains.
- A–C · 508 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 332 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 309 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 185 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ICO · Crystal structure of 6-phosphogluconolactonase from Mycobacterium tuberculosis · 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 P63338
- Elsewhere: RCSB PDB 3ICO · PDBe 3ICO · UniProt P63338
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