Research workbench
Agrobacterium tumefaciens ADP-glucose pyrophosphorylase
Analyse Agrobacterium tumefaciens ADP-glucose pyrophosphorylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W6J
- Type
- protein
- Length
- 8,228 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
- P39669
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 9 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 28% helix, 29% strand | P39669 |
| B, J, N, T, U | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 28% helix, 29% strand | P39669 |
| C | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 413 | 28% helix, 29% strand | P39669 |
| D | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 27% helix, 29% strand | P39669 |
| E, H, I, P, Q, R | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 27% helix, 28% strand | P39669 |
| K, L | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 27% helix, 30% strand | P39669 |
| O | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 29% helix, 29% strand | P39669 |
| F | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 29% helix, 30% strand | P39669 |
| G, M | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 29% helix, 29% strand | P39669 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 42 copies · chains A, B, C, D, E, H, I, J, K, L, N, O, P, Q, R, F, T, G, M, U
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 | 969 | 0.89 | 0.91 | 119 | empty |
| 2 | 1141 | 0.89 | 0.90 | 151 | empty |
| 3 | 987 | 0.89 | 0.90 | 131 | empty |
| 4 | 1093 | 0.86 | 0.86 | 118 | SO4 |
| 5 | 1192 | 0.83 | 0.84 | 130 | SO4 |
Interfaces
35 interfaces between chains.
- T–U · 1528 Ų buried · 21 hydrogen bonds · protein-protein
- H–G · 1525 Ų buried · 21 hydrogen bonds · protein-protein
- C–I · 1517 Ų buried · 20 hydrogen bonds · protein-protein
- Q–F · 1509 Ų buried · 22 hydrogen bonds · protein-protein
- B–K · 1504 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5W6J · Agrobacterium tumefaciens ADP-glucose pyrophosphorylase · 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
- Every structure of UniProt P39669
- Elsewhere: RCSB PDB 5W6J · PDBe 5W6J · UniProt P39669
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.