MolNFT v1 · #139116 · protein
Human thymidylate synthase bound with dump
5X5D: “Human thymidylate synthase bound with dump”. X-ray diffraction, 1 ligand (UMP), 19 pockets (best druggability 0.82). MolNFT v1 #139116 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X5D
- Type
- protein
- Length
- 1,712 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
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 34% helix, 23% strand | P04818 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 23% strand | P04818 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 285 | 34% helix, 23% strand | P04818 |
| E | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 35% helix, 23% strand | P04818 |
| F | Thymidylate synthase (EC 2.1.1.45) | protein | 284 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 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
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.82 | 0.83 | 91 | UMP |
| 2 | 1070 | 0.81 | 0.82 | 92 | UMP |
| 3 | 416 | 0.73 | 0.83 | 44 | UMP |
| 4 | 526 | 0.70 | 0.79 | 45 | UMP |
| 5 | 466 | 0.66 | 0.78 | 37 | UMP |
Interfaces
7 interfaces between chains.
- C–F · 2202 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2192 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2128 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 289 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5X5D · Human thymidylate synthase bound with dUMP · 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 5X5D · PDBe 5X5D · UniProt P04818
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