MolNFT v1 · #140182 · protein
Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor pgmi- 004A
5Y2I: “Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor pgmi- 004A”. X-ray diffraction, 2 ligands (8KX, CL), 6 pockets (best druggability 0.60). MolNFT v1 #140182 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y2I
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase 1
- EC
- 5.4.2.11, 5.4.2.4
- UniProt
- P18669
- Ligands
- 8KX, CL
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 233 | 45% helix, 12% strand | P18669 |
| C | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 234 | 44% helix, 13% strand | P18669 |
Ligands and binding sites
- 8KX · 3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)-~{N}-[4-(trifluoromethyl)phenyl]anthracene-2-sulfonamide · ligand · chains B
- CL · Chloride ion · ion · chains B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.60 | 0.78 | 33 | 8KX |
| 2 | 179 | 0.48 | 0.76 | 26 | MES |
| 3 | 164 | 0.43 | 0.74 | 22 | empty |
| 4 | 169 | 0.42 | 0.73 | 22 | empty |
| 5 | 93 | 0.36 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- B–C · 1070 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5Y2I · Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A · the same entry in another collection · chain B against B, TM-score 1.00
- P18669 · AlphaFold monomer V2.0 prediction for phosphoglycerate mutase 1 (P18669) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P18669
- Elsewhere: RCSB PDB 5Y2I · PDBe 5Y2I · UniProt P18669
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