MolNFT v1 · #21034 · protein
E. COLI uridine phosphorylase: 2'-deoxyuridine phosphate complex
1RXS: “E. COLI uridine phosphorylase: 2'-deoxyuridine phosphate complex”. X-ray diffraction, 4 ligands (DUR, V7O, K), 20 pockets (best druggability 0.81). MolNFT v1 #21034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RXS
- Type
- protein
- Length
- 7,352 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P12758
- Ligands
- DUR, V7O, K, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, d, L, m, o | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 29% strand | P12758 |
| a, b, c, e, G, P, h, I, j, k, l, M | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 32% helix, 30% strand | P12758 |
| B, C, D, E, F, R, H, i, J, K, N, Q, O | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 34% helix, 30% strand | P12758 |
Ligands and binding sites
- DUR · 2'-deoxyuridine · ligand · 25 copies · chains A, a, B, b, C, c, D, d, E, e, F, R, G, P, H, h, I, i, J, j, K, k, L, l, M, m, N, Q, O, o
- V7O · Meta vanadate · ligand · 20 copies · chains A, B, C, a, b, c, D, E, F, d, e, R, G, H, I, P, h, i, J, K, L, j, k, l, M, N, O, m, Q, o
- K · Potassium ion · metal · 15 copies · chains A, a, B, b, C, c, D, d, E, e, F, R, G, P, H, h, I, i, J, j, K, k, L, l, M, m, N, Q, O, o
- PO4 · Phosphate ion · ion · 25 copies · chains A, a, B, b, C, c, D, d, E, e, F, R, G, P, H, h, I, i, J, j, K, k, L, l, M, m, N, Q, O, o
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.81 | 0.82 | 89 | PO4, DUR |
| 2 | 1031 | 0.80 | 0.81 | 110 | V7O |
| 3 | 958 | 0.79 | 0.81 | 106 | V7O |
| 4 | 892 | 0.79 | 0.81 | 103 | V7O |
| 5 | 888 | 0.79 | 0.81 | 102 | V7O |
Interfaces
75 interfaces between chains.
- H–h · 2098 Ų buried · 19 hydrogen bonds · protein-protein
- I–i · 2091 Ų buried · 19 hydrogen bonds · protein-protein
- J–j · 2091 Ų buried · 19 hydrogen bonds · protein-protein
- G–P · 2089 Ų buried · 21 hydrogen bonds · protein-protein
- B–b · 2088 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1RXS · E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex · the same entry in another collection · chain F against F, 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 P12758
- Elsewhere: RCSB PDB 1RXS · PDBe 1RXS · UniProt P12758
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