Research workbench
Crystal structure of human aprt wild type in complex with gmp
Analyse Crystal structure of human aprt wild type in complex with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HGS
- Type
- protein
- Length
- 349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- P07741
- Ligands
- 5GP
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 176 | 36% helix, 35% strand | P07741 |
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 173 | 36% helix, 33% strand | P07741 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.63 | 0.78 | 34 | 5GP |
| 2 | 318 | 0.60 | 0.77 | 37 | 5GP |
| 3 | 111 | 0.42 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1536 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6HGS · Crystal Structure of Human APRT wild type in complex with GMP · the same entry in another collection · chain A against A, TM-score 1.00
- P07741 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase (P07741) · a predicted model of the same protein · chain B 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 P07741
- Elsewhere: RCSB PDB 6HGS · PDBe 6HGS · UniProt P07741
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