MolNFT v1 · #99684 · protein
Crystal structure of purine nucleoside phosphorylase from meiothermus ruber dsm 1279 complexed with sulfate.
4MAR · Purine nucleoside phosphorylase deod-type: “Crystal structure of purine nucleoside phosphorylase from meiothermus ruber dsm 1279 complexed with sulfate.”. X-ray diffraction, 2 ligands (MG, SO4), 8 pockets (best druggability 0.68).…
- PDB
- 4MAR
- Type
- protein
- Length
- 693 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- D3PPS9
- Ligands
- MG, SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 231 | 35% helix, 29% strand | D3PPS9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.68 | 0.80 | 43 | SO4 |
| 2 | 398 | 0.67 | 0.80 | 47 | SO4 |
| 3 | 162 | 0.59 | 0.83 | 29 | empty |
| 4 | 124 | 0.55 | 0.82 | 25 | empty |
| 5 | 197 | 0.55 | 0.79 | 29 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1577 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1448 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4MAR · Crystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279… · 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 D3PPS9
- Elsewhere: RCSB PDB 4MAR · PDBe 4MAR · UniProt D3PPS9
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