Research workbench
Crystal structure of adenine phosphoribosyltransferase from francisella tularensis in complex with adenine
Analyse Crystal structure of adenine phosphoribosyltransferase from francisella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YW5
- Type
- protein
- Length
- 699 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
- ADE
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 178 | 33% helix, 31% strand | A0A0E2ZLA9 |
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 171 | 34% helix, 29% strand | A0A0E2ZLA9 |
| C, D | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 175 | 32% helix, 33% strand | A0A0E2ZLA9 |
Ligands and binding sites
- ADE · Adenine · ligand · 4 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.75 | 0.82 | 60 | empty |
| 2 | 451 | 0.67 | 0.79 | 47 | ADE |
| 3 | 69 | 0.67 | 0.94 | 31 | empty |
| 4 | 433 | 0.65 | 0.78 | 43 | ADE |
| 5 | 385 | 0.63 | 0.78 | 45 | ADE |
Interfaces
5 interfaces between chains.
- B–C · 1415 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1407 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 206 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 130 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 119 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YW5 · Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis in… · 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 5YW5 · PDBe 5YW5 · UniProt A0A0E2ZLA9
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