MolNFT v1 · #167642 · protein
Agrobacterium tumefaciens ADP-glucose pyrophosphorylase W106A
6VR0 · Glucose-1-phosphate adenylyltransferase: “Agrobacterium tumefaciens ADP-glucose pyrophosphorylase W106A”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.89). MolNFT v1 #167642 on GenesisL1: 3D structure, binding…
- PDB
- 6VR0
- Type
- protein
- Length
- 4,040 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate adenylyltransferase
- EC
- 2.7.7.27
- UniProt
- A0A083ZTG5
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 404 | 29% helix, 28% strand | A0A083ZTG5 |
| B, F | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 403 | 28% helix, 29% strand | A0A083ZTG5 |
| C, D, G, H, I, J | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 404 | 29% helix, 29% strand | A0A083ZTG5 |
| E | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 406 | 29% helix, 28% strand | A0A083ZTG5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 89 copies · chains A, G, B, C, F, D, J, E, H, I
- GOL · Glycerol · additive · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.89 | 0.91 | 124 | empty |
| 2 | 892 | 0.80 | 0.82 | 100 | SO4 |
| 3 | 181 | 0.78 | 0.93 | 32 | empty |
| 4 | 168 | 0.78 | 0.94 | 26 | empty |
| 5 | 203 | 0.77 | 0.92 | 31 | empty |
Interfaces
14 interfaces between chains.
- A–D · 1531 Ų buried · 22 hydrogen bonds · protein-protein
- G–J · 1509 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 1473 Ų buried · 21 hydrogen bonds · protein-protein
- D–J · 979 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 967 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6VR0 · Agrobacterium Tumefaciens ADP-glucose pyrophosphorylase W106A · 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
- Every structure of UniProt A0A083ZTG5
- Elsewhere: RCSB PDB 6VR0 · PDBe 6VR0 · UniProt A0A083ZTG5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.