MolNFT v1 · #27248 · protein
Crystal structure of purine nucleoside phosphorylase deod from bacillus anthracis
1XE3: “Crystal structure of purine nucleoside phosphorylase deod from bacillus anthracis”. X-ray diffraction, 1 ligand (CL), 17 pockets (best druggability 0.83). MolNFT v1 #27248 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1XE3
- Type
- protein
- Length
- 1,402 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q81T09
- Ligands
- CL
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 233 | 36% helix, 29% strand | Q81T09 |
| B, F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 233 | 35% helix, 28% strand | Q81T09 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 234 | 35% helix, 29% strand | Q81T09 |
| D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 235 | 36% helix, 29% strand | Q81T09 |
| E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 234 | 35% helix, 29% strand | Q81T09 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.83 | 0.85 | 90 | empty |
| 2 | 439 | 0.71 | 0.81 | 38 | empty |
| 3 | 444 | 0.69 | 0.80 | 43 | empty |
| 4 | 437 | 0.69 | 0.80 | 40 | empty |
| 5 | 455 | 0.68 | 0.79 | 40 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1744 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 1735 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1729 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1424 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1421 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1XE3 · Crystal Structure of purine nucleoside phosphorylase DeoD from Bacillus anthracis · the same entry in another collection · chain F against F, TM-score 1.00
- Q81T09 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (Q81T09) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q81T09
- Elsewhere: RCSB PDB 1XE3 · PDBe 1XE3 · UniProt Q81T09
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