MolNFT v1 · #141096 · protein
Crystal structure of adenine phosphoribosyltransferase from francisella tularensis.
5YW2: “Crystal structure of adenine phosphoribosyltransferase from francisella tularensis.”. X-ray diffraction, 3 ligands (MG, CL, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #141096 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YW2
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- A0A0E2ZLA9
- Ligands
- MG, CL, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 178 | 32% helix, 34% strand | A0A0E2ZLA9 |
| C | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 179 | 32% helix, 32% strand | A0A0E2ZLA9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.70 | 0.79 | 45 | SO4, CL |
| 2 | 709 | 0.69 | 0.76 | 59 | SO4, CL |
| 3 | 618 | 0.68 | 0.77 | 69 | MG |
| 4 | 490 | 0.66 | 0.77 | 37 | CL, SO4 |
| 5 | 497 | 0.65 | 0.77 | 39 | SO4, CL |
Interfaces
4 interfaces between chains.
- C–D · 1449 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 20 hydrogen bonds · protein-protein
- C–B · 399 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 90 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YW2 · Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis. · 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 A0A0E2ZLA9
- Elsewhere: RCSB PDB 5YW2 · PDBe 5YW2 · UniProt A0A0E2ZLA9
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