MolNFT v1 · #50266 · protein
Human thymidylate synthase stabilized in active conformation by R163K mutation: asymmetry and reactivity of CYS195
2RD8: “Human thymidylate synthase stabilized in active conformation by R163K mutation: asymmetry and reactivity of…”. X-ray diffraction, 1 ligand (PO4), 10 pockets (best druggability 0.63). MolNFT v1 #50266 on GenesisL1: 3D structure…
- PDB
- 2RD8
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 283 | 34% helix, 24% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 282 | 33% helix, 21% strand | P04818 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.63 | 0.76 | 43 | BME, PO4 |
| 2 | 349 | 0.61 | 0.77 | 36 | PO4 |
| 3 | 91 | 0.45 | 0.80 | 19 | empty |
| 4 | 57 | 0.40 | 0.81 | 14 | empty |
| 5 | 92 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2181 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 2RD8 · Human Thymidylate Synthase Stabilized in Active Conformation by R163K Mutation: Asymmetry… · the same entry in another collection · chain B against B, 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 2RD8 · PDBe 2RD8 · UniProt P04818
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