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Crystal structure of purine nucleoside phosphorylase from meiothermus ruber dsm 1279, nysgrc target 029804.
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
- 4M3N
- 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, PO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 34% 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 | 34% 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.68 | 0.79 | 43 | empty |
| 2 | 431 | 0.66 | 0.79 | 50 | empty |
| 3 | 169 | 0.59 | 0.82 | 26 | empty |
| 4 | 248 | 0.55 | 0.77 | 32 | empty |
| 5 | 179 | 0.53 | 0.79 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1566 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1498 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4M3N · 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 4M3N · PDBe 4M3N · UniProt D3PPS9
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