MolNFT v1 · #20559 · protein
Crystal structure of phosphoglycerate mutase from M. tuberculosis
1RII · 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase: “Crystal structure of phosphoglycerate mutase from M. tuberculosis”. X-ray diffraction, 16 pockets (best druggability 0.74). MolNFT v1 #20559 on GenesisL1: 3D structure…
- PDB
- 1RII
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
- EC
- 5.4.2.1
- UniProt
- P0A5R6
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 243 | 45% helix, 12% strand | P0A5R6 |
| B | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 237 | 45% helix, 12% strand | P0A5R6 |
| C | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 237 | 41% helix, 11% strand | P0A5R6 |
| D | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.1) | protein | 231 | 43% helix, 11% strand | P0A5R6 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.74 | 0.98 | 21 | empty |
| 2 | 336 | 0.71 | 0.84 | 35 | empty |
| 3 | 52 | 0.71 | 0.98 | 20 | empty |
| 4 | 240 | 0.70 | 0.86 | 37 | GOL |
| 5 | 305 | 0.70 | 0.84 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 860 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 855 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 494 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 111 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1RII · Crystal structure of phosphoglycerate mutase from M. 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 P0A5R6
- Elsewhere: RCSB PDB 1RII · PDBe 1RII · UniProt P0A5R6
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