MolNFT v1 · #13043 · protein
Crystal structure of ECTS/DUMP/THF complex
1KZI · Thymidylate synthase: “Crystal structure of ECTS/DUMP/THF complex”. X-ray diffraction, 3 ligands (UMP, THG, CO3), 6 pockets (best druggability 0.77). MolNFT v1 #13043 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KZI
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P0A884
- Ligands
- UMP, THG, CO3
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 36% helix, 26% strand | P0A884 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- THG · (6S)-5,6,7,8-tetrahydrofolate · ligand · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 3 copies · chains A
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A
- GOL · Glycerol · additive · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.77 | 0.85 | 49 | UMP, THG |
| 2 | 370 | 0.77 | 0.87 | 44 | UMP, THG |
| 3 | 108 | 0.44 | 0.78 | 20 | empty |
| 4 | 87 | 0.44 | 0.80 | 17 | empty |
| 5 | 103 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2380 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 modified (covalent ligand, carboxylation, additive adduct).
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 P0A884
- Elsewhere: RCSB PDB 1KZI · PDBe 1KZI · UniProt P0A884
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