MolNFT v1 · #105373 · protein
Crystal structure of a putative uridine phosphorylase from actinobacillus succinogenes 130Z (target nysgrc-029667 )
4R31: “Crystal structure of a putative uridine phosphorylase from actinobacillus succinogenes 130Z (target…”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #105373 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4R31
- Type
- protein
- Length
- 1,522 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- A6VLF7
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 259 | 36% helix, 27% strand | A6VLF7 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 254 | 35% helix, 28% strand | A6VLF7 |
| C, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 253 | 34% helix, 28% strand | A6VLF7 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 28% strand | A6VLF7 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 35% helix, 28% strand | A6VLF7 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, D, E, B, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.78 | 0.84 | 56 | GOL |
| 2 | 454 | 0.75 | 0.84 | 48 | GOL |
| 3 | 465 | 0.74 | 0.83 | 46 | GOL |
| 4 | 422 | 0.72 | 0.83 | 41 | GOL |
| 5 | 419 | 0.72 | 0.82 | 42 | GOL |
Interfaces
12 interfaces between chains.
- A–D · 2106 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1910 Ų buried · 23 hydrogen bonds · protein-protein
- B–F · 1885 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1142 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1132 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 4R31 · Crystal structure of a putative uridine phosphorylase from Actinobacillus succinogenes… · 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 A6VLF7
- Elsewhere: RCSB PDB 4R31 · PDBe 4R31 · UniProt A6VLF7
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