MolNFT v1 · #140193 · protein
X-ray structure of phosphoglycerate mutase 1(PGAM1) complexed with a small molecule
5Y2U: “X-ray structure of phosphoglycerate mutase 1(PGAM1) complexed with a small molecule”. X-ray diffraction, 2 ligands (AZN, CL), 5 pockets (best druggability 0.62). MolNFT v1 #140193 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Y2U
- Type
- protein
- Length
- 471 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
- AZN, CL
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 237 | 44% helix, 12% strand | P18669 |
| C | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 234 | 42% helix, 13% strand | P18669 |
Ligands and binding sites
- AZN · Alizarin red · ligand · 2 copies · chains B, C
- 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.62 | 0.78 | 34 | AZN |
| 2 | 366 | 0.59 | 0.76 | 38 | AZN, MES |
| 3 | 118 | 0.45 | 0.78 | 14 | empty |
| 4 | 154 | 0.44 | 0.75 | 22 | empty |
| 5 | 122 | 0.40 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- B–C · 1082 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5Y2U · X-ray structure of Phosphoglycerate Mutase 1(PGAM1) complexed with a small molecule · 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 5Y2U · PDBe 5Y2U · UniProt P18669
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