MolNFT v1 · #93405 · protein
Structure of human thymidylate synthase at low salt conditions
4H1I: “Structure of human thymidylate synthase at low salt conditions”. X-ray diffraction, 1 ligand (SO4), 18 pockets (best druggability 0.64). MolNFT v1 #93405 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4H1I
- Type
- protein
- Length
- 1,124 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 32% helix, 23% strand | P04818 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.64 | 0.77 | 36 | SO4 |
| 2 | 421 | 0.63 | 0.77 | 43 | SO4 |
| 3 | 432 | 0.62 | 0.77 | 43 | SO4 |
| 4 | 410 | 0.62 | 0.77 | 35 | SO4 |
| 5 | 308 | 0.55 | 0.75 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2319 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 2285 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 420 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 103 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4H1I · Structure of human thymidylate synthase at low salt conditions · 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 4H1I · PDBe 4H1I · UniProt P04818
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