Research workbench
Crystal structure of purine nucleoside phosphorylase from meiothermus ruber dsm 1279 complexed with sulfate.
Analyse Crystal structure of purine nucleoside phosphorylase from meiothermus ruber dsm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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