MolNFT v1 · #99339 · protein
Crystal structure of adenine phosphoribosyltransferase from rhodothermus marinus dsm 4252, nysgrc target 029775.
4M0K: “Crystal structure of adenine phosphoribosyltransferase from rhodothermus marinus dsm 4252, nysgrc target…”. X-ray diffraction, 2 ligands (AMP, CA), 3 pockets (best druggability 0.77). MolNFT v1 #99339 on GenesisL1: 3D structure…
- PDB
- 4M0K
- 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
- D0MGF4
- Ligands
- AMP, CA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 173 | 34% helix, 34% strand | D0MGF4 |
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 174 | 33% helix, 34% strand | D0MGF4 |
| C, D | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 176 | 36% helix, 34% strand | D0MGF4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.77 | 0.79 | 71 | AMP |
| 2 | 1048 | 0.77 | 0.79 | 81 | AMP |
| 3 | 110 | 0.52 | 0.82 | 22 | CA |
Interfaces
3 interfaces between chains.
- C–D · 1496 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1466 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4M0K · Crystal structure of adenine phosphoribosyltransferase from Rhodothermus marinus DSM… · 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 D0MGF4
- Elsewhere: RCSB PDB 4M0K · PDBe 4M0K · UniProt D0MGF4
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