MolNFT v1 · #106889 · protein
Crystal structure of double mutant E. COLI purine nucleoside phosphorylase with 2 fmc molecules
4TTA · Purine nucleoside phosphorylase deod-type: “Crystal structure of double mutant E. COLI purine nucleoside phosphorylase with 2 fmc molecules”. X-ray diffraction, 3 ligands (FMC, PO4, SO4), 13 pockets (best druggability 0.79). MolNFT…
- PDB
- 4TTA
- Type
- protein
- Length
- 1,409 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- U0SVH6
- Ligands
- FMC, PO4, SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 37% helix, 29% strand | U0SVH6 |
| C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 224 | 36% helix, 29% strand | U0SVH6 |
Ligands and binding sites
- FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · ligand · 2 copies · chains C, F, A, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, D, B, E, C, F
- SO4 · Sulfate ion · ion · 6 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.79 | 0.81 | 107 | FMC, PO4 |
| 2 | 313 | 0.74 | 0.86 | 48 | PO4 |
| 3 | 312 | 0.72 | 0.85 | 44 | PO4 |
| 4 | 528 | 0.71 | 0.80 | 51 | PO4 |
| 5 | 458 | 0.70 | 0.80 | 54 | PO4, FMC |
Interfaces
12 interfaces between chains.
- C–E · 1777 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1770 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1763 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 1717 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 1698 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4TTA · Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 2 FMC… · 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 U0SVH6
- Elsewhere: RCSB PDB 4TTA · PDBe 4TTA · UniProt U0SVH6
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