MolNFT v1 · #137025 · protein
Crystal structure of the R515W missense variant of human PGM1
5VBI · Phosphoglucomutase-1: “Crystal structure of the R515W missense variant of human PGM1”. X-ray diffraction, 2 ligands (MG, SO4), 10 pockets (best druggability 0.70). MolNFT v1 #137025 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VBI
- Type
- protein
- Length
- 1,125 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglucomutase-1
- EC
- 5.4.2.2
- UniProt
- P36871
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglucomutase-1 (EC 5.4.2.2) | protein | 563 | 37% helix, 26% strand | P36871 |
| B | Phosphoglucomutase-1 (EC 5.4.2.2) | protein | 562 | 36% helix, 25% strand | P36871 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.70 | 0.78 | 63 | GOL |
| 2 | 616 | 0.68 | 0.77 | 64 | SO4, GOL |
| 3 | 324 | 0.58 | 0.77 | 44 | empty |
| 4 | 124 | 0.39 | 0.74 | 26 | GOL |
| 5 | 104 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 270 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
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 P36871
- Elsewhere: RCSB PDB 5VBI · PDBe 5VBI · UniProt P36871
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