Research workbench
Crystal structure of purine nucleoside phosphorylase from porphyromonas gingivalis atcc 33277, nysgrc target 030972, orthorhombic symmetry
Analyse Crystal structure of purine nucleoside phosphorylase from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NSN
- Type
- protein
- Length
- 819 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- B2RKN6
- Ligands
- ADE, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 273 | 36% helix, 24% strand | B2RKN6 |
Ligands and binding sites
- ADE · Adenine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.79 | 0.84 | 74 | empty |
| 2 | 104 | 0.78 | 0.98 | 26 | ADE, SO4 |
| 3 | 100 | 0.77 | 0.98 | 25 | ADE, SO4 |
| 4 | 97 | 0.77 | 0.98 | 25 | ADE, SO4 |
| 5 | 73 | 0.33 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1130 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1129 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1123 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered, oxidation).
Compared structures
- 4NSN · Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC… · 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 B2RKN6
- Elsewhere: RCSB PDB 4NSN · PDBe 4NSN · UniProt B2RKN6
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