MolNFT v1 · #180750 · protein
Crystal structure of phosphoglycerate kinase from mycobacterium avium
7LA1: “Crystal structure of phosphoglycerate kinase from mycobacterium avium”. X-ray diffraction, 12 pockets (best druggability 0.85). MolNFT v1 #180750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LA1
- Type
- protein
- Length
- 1,644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- A0QHY4
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 412 | 43% helix, 16% strand | A0QHY4 |
| B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 411 | 42% helix, 16% strand | A0QHY4 |
| D | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 409 | 43% helix, 16% strand | A0QHY4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.85 | 0.86 | 111 | EDO |
| 2 | 301 | 0.77 | 0.89 | 41 | empty |
| 3 | 594 | 0.77 | 0.83 | 67 | EDO |
| 4 | 298 | 0.77 | 0.89 | 50 | EDO |
| 5 | 460 | 0.76 | 0.85 | 69 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1829 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1555 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 494 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LA1 · Crystal structure of phosphoglycerate kinase from Mycobacterium avium · the same entry in another collection · chain A against A, TM-score 1.00
- A0QHY4 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (A0QHY4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A0QHY4
- Elsewhere: RCSB PDB 7LA1 · PDBe 7LA1 · UniProt A0QHY4
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