MolNFT v1 · #139113 · protein
Human thymidylate synthase bound with phosphate ion
5X5A: “Human thymidylate synthase bound with phosphate ion”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.81). MolNFT v1 #139113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X5A
- Type
- protein
- Length
- 1,692 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 287 | 34% helix, 23% strand | P04818 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 35% helix, 23% strand | P04818 |
| D, E, F | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 35% helix, 24% strand | P04818 |
Ligands and binding sites
- PO4 · Phosphate 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
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.81 | 0.82 | 83 | PO4 |
| 2 | 987 | 0.80 | 0.82 | 96 | PO4 |
| 3 | 430 | 0.65 | 0.78 | 47 | PO4 |
| 4 | 415 | 0.63 | 0.77 | 47 | PO4 |
| 5 | 390 | 0.63 | 0.78 | 35 | PO4 |
Interfaces
7 interfaces between chains.
- B–E · 2177 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2166 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 2114 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 266 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5X5A · Human thymidylate synthase bound with phosphate ion · 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 P04818
- Elsewhere: RCSB PDB 5X5A · PDBe 5X5A · UniProt P04818
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