MolNFT v1 · #139126 · protein
Human thymidylate synthase complexed with dump and raltitrexed
5X5Q: “Human thymidylate synthase complexed with dump and raltitrexed”. X-ray diffraction, 2 ligands (UMP, D16), 19 pockets (best druggability 0.83). MolNFT v1 #139126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X5Q
- Type
- protein
- Length
- 1,694 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
- UMP, D16
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 35% helix, 23% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 287 | 34% helix, 23% strand | P04818 |
| C, E | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 36% helix, 23% strand | P04818 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 37% helix, 24% strand | P04818 |
| F | Thymidylate synthase (EC 2.1.1.45) | protein | 280 | 36% helix, 24% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, D, B, E, C, F
- D16 · Tomudex · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.83 | 0.84 | 89 | UMP, D16 |
| 2 | 974 | 0.82 | 0.83 | 94 | UMP, D16 |
| 3 | 610 | 0.69 | 0.77 | 61 | UMP, D16 |
| 4 | 502 | 0.67 | 0.78 | 50 | UMP, D16 |
| 5 | 403 | 0.67 | 0.80 | 36 | UMP, D16 |
Interfaces
7 interfaces between chains.
- C–F · 2232 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 2222 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2201 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 327 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 5X5Q · PDBe 5X5Q · UniProt P04818
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