Research workbench
Agrobacterium tumefaciens ADP-glucose pyrophosphorylase P96A mutant bound to activator pyruvate
Analyse Agrobacterium tumefaciens ADP-glucose pyrophosphorylase P96A mutant bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W5R
- Type
- protein
- Length
- 8,229 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
- PYR, 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 | 27% helix, 29% strand | P39669 |
| B, C, J, N, T, U | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 415 | 28% helix, 29% strand | P39669 |
| D | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 28% helix, 29% strand | P39669 |
| E, H, I, P, Q, R | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 28% helix, 29% strand | P39669 |
| K, L | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 29% helix, 29% strand | P39669 |
| O | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 27% helix, 28% strand | P39669 |
| F | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 28% helix, 29% strand | P39669 |
| G | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 29% helix, 30% strand | P39669 |
| M | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 29% helix, 30% strand | P39669 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 9 copies · chains A, P, D, M, E, H, G, C, I, J, B, K, Q, F, T, U
- SO4 · Sulfate ion · ion · 42 copies · chains A, B, C, D, E, H, I, J, K, L, N, O, P, Q, R, F, G, M, T, 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 | 1055 | 0.89 | 0.91 | 138 | empty |
| 2 | 1064 | 0.89 | 0.91 | 144 | PYR |
| 3 | 1026 | 0.89 | 0.90 | 141 | PYR |
| 4 | 1114 | 0.85 | 0.86 | 137 | SO4 |
| 5 | 680 | 0.80 | 0.85 | 61 | empty |
Interfaces
35 interfaces between chains.
- B–K · 1538 Ų buried · 19 hydrogen bonds · protein-protein
- D–M · 1532 Ų buried · 26 hydrogen bonds · protein-protein
- T–U · 1521 Ų buried · 21 hydrogen bonds · protein-protein
- H–G · 1510 Ų buried · 24 hydrogen bonds · protein-protein
- C–I · 1505 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5W5R · Agrobacterium tumefaciens ADP-glucose pyrophosphorylase P96A mutant bound to activator… · the same entry in another collection · chain L against L, 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 5W5R · PDBe 5W5R · UniProt P39669
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