MolNFT v1 · #138007 · protein
Agrobacterium tumefaciens ADP-glucose pyrophosphorylase bound to activator ethyl pyruvate
5W5T · Glucose-1-phosphate adenylyltransferase: “Agrobacterium tumefaciens ADP-glucose pyrophosphorylase bound to activator ethyl pyruvate”. X-ray diffraction, 2 ligands (9X7, SO4), 20 pockets (best druggability 0.88). MolNFT v1 #138007 on…
- PDB
- 5W5T
- Type
- protein
- Length
- 8,205 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
- 9X7, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 17 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 | 407 | 28% helix, 30% strand | P39669 |
| B | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 28% helix, 30% strand | P39669 |
| C | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 28% helix, 30% strand | P39669 |
| D, J, L | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 28% helix, 30% strand | P39669 |
| E | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 28% helix, 29% strand | P39669 |
| F, N | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 28% helix, 29% strand | P39669 |
| G | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 411 | 28% helix, 29% strand | P39669 |
| H | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 27% helix, 29% strand | P39669 |
| I | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 28% helix, 29% strand | P39669 |
| K | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 28% helix, 30% strand | P39669 |
| M | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 28% helix, 30% strand | P39669 |
| O | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 27% helix, 30% strand | P39669 |
| P | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 413 | 28% helix, 30% strand | P39669 |
| Q | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 410 | 28% helix, 30% strand | P39669 |
| R | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 412 | 28% helix, 29% strand | P39669 |
| Z | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 408 | 29% helix, 30% strand | P39669 |
| T | Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27) | protein | 409 | 29% helix, 30% strand | P39669 |
Ligands and binding sites
- 9X7 · ethyl 2-oxopropanoate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, Z, T
- SO4 · Sulfate ion · ion · 75 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, Z, T
- GOL · Glycerol · additive · 46 copies · chains A, B, D, C, E, G, H, I, J, M, N, K, L, O, P, Q, R, Z, 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 | 967 | 0.88 | 0.90 | 144 | 9X7 |
| 2 | 879 | 0.88 | 0.90 | 112 | GOL |
| 3 | 541 | 0.86 | 0.92 | 94 | empty |
| 4 | 1015 | 0.81 | 0.82 | 110 | SO4, 9X7 |
| 5 | 1052 | 0.80 | 0.82 | 101 | SO4, GOL |
Interfaces
34 interfaces between chains.
- E–F · 1542 Ų buried · 21 hydrogen bonds · protein-protein
- Q–R · 1534 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1531 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1528 Ų buried · 23 hydrogen bonds · protein-protein
- O–P · 1518 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5W5T · Agrobacterium tumefaciens ADP-Glucose Pyrophosphorylase bound to activator ethyl pyruvate · the same entry in another collection · chain K against K, 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 5W5T · PDBe 5W5T · UniProt P39669
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