MolNFT v1 · #127473 · protein
The X-ray structure of human M190I phosphoglycerate kinase 1 mutant
5MXM: “The X-ray structure of human M190I phosphoglycerate kinase 1 mutant”. X-ray diffraction, 3 ligands (3PG, ADP, MG), 3 pockets (best druggability 0.72). MolNFT v1 #127473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MXM
- Type
- protein
- Length
- 415 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase 1
- EC
- 2.7.2.3
- UniProt
- P00558
- Ligands
- 3PG, ADP, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 415 | 40% helix, 18% strand | P00558 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.72 | 0.80 | 64 | MG, 3PG, ADP |
| 2 | 72 | 0.32 | 0.74 | 14 | empty |
| 3 | 61 | 0.31 | 0.75 | 13 | empty |
Compared structures
- 5MXM · The X-ray structure of human M190I phosphoglycerate kinase 1 mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P00558 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 1 (P00558) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P00558
- Elsewhere: RCSB PDB 5MXM · PDBe 5MXM · UniProt P00558
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.