Research workbench
Agrobacterium tumefaciens ADP-glucose pyrophosphorylase- S72D in the presence of sulfate
Analyse Agrobacterium tumefaciens ADP-glucose pyrophosphorylase- S72D in the presence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V99
- Type
- protein
- Length
- 8,300 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate adenylyltransferase
- EC
- 2.7.7.27
- UniProt
- Q8U8L5
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, W, T | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 28% helix, 29% strand | Q8U8L5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 136 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, W, T
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 | 1075 | 0.89 | 0.90 | 144 | empty |
| 2 | 998 | 0.89 | 0.90 | 131 | empty |
| 3 | 810 | 0.88 | 0.91 | 99 | empty |
| 4 | 258 | 0.82 | 0.94 | 28 | empty |
| 5 | 279 | 0.82 | 0.93 | 28 | empty |
Interfaces
34 interfaces between chains.
- C–D · 1511 Ų buried · 23 hydrogen bonds · protein-protein
- W–T · 1498 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 22 hydrogen bonds · protein-protein
- Q–R · 1480 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1476 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6V99 · Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase- S72D in the presence of sulfate · the same entry in another collection · chain J against J, 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 Q8U8L5
- Elsewhere: RCSB PDB 6V99 · PDBe 6V99 · UniProt Q8U8L5
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