Research workbench
Adenosine triphosphate phosphoribosyltransferase from vibrio cholerae in complex with ATP and prpp
Analyse Adenosine triphosphate phosphoribosyltransferase from vibrio cholerae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DAH
- Type
- protein
- Length
- 1,735 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- C3LU29
- Ligands
- ATP, PRP, MG, PO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 288 | 32% helix, 27% strand | C3LU29 |
| B | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 292 | 33% helix, 30% strand | C3LU29 |
| C | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 288 | 32% helix, 28% strand | C3LU29 |
| D | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 287 | 32% helix, 28% strand | C3LU29 |
| E | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 293 | 33% helix, 30% strand | C3LU29 |
| F | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 287 | 33% helix, 28% strand | C3LU29 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, F
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, C, D, F
- MG · Magnesium ion · metal · 2 copies · chains C, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, D, F, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
- GOL · Glycerol · additive · 2 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.70 | 0.76 | 90 | GOL, EDO, PO4, MG, PRP |
| 2 | 508 | 0.67 | 0.78 | 44 | empty |
| 3 | 533 | 0.65 | 0.77 | 54 | EDO, GOL |
| 4 | 492 | 0.65 | 0.77 | 42 | PEG |
| 5 | 161 | 0.61 | 0.84 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1130 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1126 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 973 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 952 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7DAH · Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP… · 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 C3LU29
- Elsewhere: RCSB PDB 7DAH · PDBe 7DAH · UniProt C3LU29
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