MolNFT v1 · #83870 · protein
Structure of ATP grasp protein
3WVQ · PGM1: “Structure of ATP grasp protein”. X-ray diffraction, 1 ligand (SO4), 19 pockets (best druggability 0.81). MolNFT v1 #83870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WVQ
- Type
- protein
- Length
- 1,715 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGM1
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | PGM1 | protein | 433 | 37% helix, 24% strand | — |
| B | PGM1 | protein | 422 | 37% helix, 24% strand | — |
| C | PGM1 | protein | 427 | 37% helix, 23% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.81 | 0.86 | 83 | SO4 |
| 2 | 622 | 0.81 | 0.86 | 69 | SO4 |
| 3 | 793 | 0.77 | 0.81 | 73 | SO4 |
| 4 | 515 | 0.77 | 0.84 | 93 | empty |
| 5 | 918 | 0.77 | 0.80 | 78 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1253 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1247 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 244 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 147 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3WVQ · Structure of ATP grasp protein · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3WVQ · PDBe 3WVQ
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