MolNFT v1 · #101481 · protein
Crystal structure of purine nucleoside phosphorylase from porphyromonas gingivalis atcc 33277, nysgrc target 030972, orthorhombic symmetry
4NSN: “Crystal structure of purine nucleoside phosphorylase from porphyromonas gingivalis atcc 33277, nysgrc target…”. X-ray diffraction, 2 ligands (ADE, SO4), 7 pockets (best druggability 0.79). MolNFT v1 #101481 on GenesisL1: 3D…
- 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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