MolNFT v1 · #162217 · protein
Crystal structure of the human thymidylate synthase (hts) interface variant Q62R
6R2E: “Crystal structure of the human thymidylate synthase (hts) interface variant Q62R”. X-ray diffraction, 3 ligands (FFO, SO4, CL), 20 pockets (best druggability 0.75). MolNFT v1 #162217 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6R2E
- Type
- protein
- Length
- 2,305 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- FFO, SO4, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, H, E, G | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 34% helix, 23% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 289 | 33% helix, 23% strand | P04818 |
Ligands and binding sites
- FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 8 copies · chains A, C, D, B, F, H, E, G
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D, G, E, F, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, G
- GOL · Glycerol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.75 | 0.78 | 79 | SO4 |
| 2 | 833 | 0.75 | 0.79 | 82 | SO4 |
| 3 | 270 | 0.75 | 0.88 | 35 | FFO |
| 4 | 263 | 0.73 | 0.87 | 31 | FFO |
| 5 | 269 | 0.73 | 0.87 | 31 | FFO |
Interfaces
10 interfaces between chains.
- A–B · 2119 Ų buried · 24 hydrogen bonds · protein-protein
- H–G · 2104 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2096 Ų buried · 23 hydrogen bonds · protein-protein
- F–E · 2090 Ų buried · 26 hydrogen bonds · protein-protein
- D–G · 316 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (artifact, methylation).
Compared structures
- 6R2E · Crystal structure of the human thymidylate synthase (hTS) interface variant Q62R · the same entry in another collection · chain G against G, TM-score 1.00
- P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 6R2E · PDBe 6R2E · UniProt P04818
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