MolNFT v1 · #83871 · protein
Structure of ATP grasp protein with AMP
3WVR · PGM1: “Structure of ATP grasp protein with AMP”. X-ray diffraction, 2 ligands (AMP, SO4), 19 pockets (best druggability 0.80). MolNFT v1 #83871 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WVR
- Type
- protein
- Length
- 1,705 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGM1
- Ligands
- AMP, SO4
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PGM1 | protein | 427 | 37% helix, 24% strand | — |
| B | PGM1 | protein | 430 | 37% helix, 24% strand | — |
| C | PGM1 | protein | 433 | 36% helix, 24% strand | — |
| D | PGM1 | protein | 415 | 38% helix, 25% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.80 | 0.84 | 90 | SO4 |
| 2 | 539 | 0.80 | 0.86 | 66 | empty |
| 3 | 996 | 0.78 | 0.80 | 118 | empty |
| 4 | 710 | 0.76 | 0.81 | 65 | SO4 |
| 5 | 785 | 0.75 | 0.80 | 78 | SO4, AMP |
Interfaces
5 interfaces between chains.
- B–C · 1272 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1243 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3WVR · Structure of ATP grasp protein with AMP · the same entry in another collection · chain B against B, 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 3WVR · PDBe 3WVR
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