Research workbench
Crystal structure of purine nucleoside phosphorylase from porphyromonas gingivalis atcc 33277, nysgrc target 30972
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
- 4NS1
- Type
- protein
- Length
- 1,074 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- B2RKN6
- Ligands
- DA, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 268 | 35% helix, 24% strand | B2RKN6 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 36% helix, 24% strand | B2RKN6 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 266 | 35% helix, 25% strand | B2RKN6 |
| D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 36% helix, 24% strand | B2RKN6 |
Ligands and binding sites
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.79 | 0.85 | 68 | empty |
| 2 | 519 | 0.65 | 0.77 | 61 | DA, SO4 |
| 3 | 290 | 0.64 | 0.81 | 40 | DA, SO4 |
| 4 | 252 | 0.63 | 0.81 | 33 | DA, SO4 |
| 5 | 253 | 0.62 | 0.81 | 34 | DA, SO4 |
Interfaces
4 interfaces between chains.
- A–C · 1093 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1080 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1057 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 341 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered, oxidation).
Compared structures
- 4NS1 · 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 4NS1 · PDBe 4NS1 · UniProt B2RKN6
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