MolNFT v1 · #162063 · protein
Crystal structure of his-tag human thymidylate synthase (ht-hts) in complex with dump
6QXH: “Crystal structure of his-tag human thymidylate synthase (ht-hts) in complex with dump”. X-ray diffraction, 3 ligands (UMP, CL, SO4), 6 pockets (best druggability 0.82). MolNFT v1 #162063 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QXH
- Type
- protein
- Length
- 862 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, CL, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 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 | 288 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.82 | 0.83 | 93 | UMP, SO4 |
| 2 | 746 | 0.78 | 0.82 | 57 | UMP, PEG, CL |
| 3 | 440 | 0.75 | 0.84 | 36 | UMP |
| 4 | 163 | 0.45 | 0.75 | 24 | empty |
| 5 | 79 | 0.38 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2163 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 306 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 233 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 6QXH · Crystal structure of His-tag human thymidylate synthase (HT-hTS) in complex 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 6QXH · PDBe 6QXH · UniProt P04818
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