MolNFT v1 · #50268 · protein
Human thymidylate synthase stabilized in active conformation by R163K mutation: asymmetry and reactivity of CYS195
2RDA: “Human thymidylate synthase stabilized in active conformation by R163K mutation: asymmetry and reactivity of…”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.67). MolNFT v1 #50268 on GenesisL1: 3D structure…
- PDB
- 2RDA
- Type
- protein
- Length
- 1,687 residues
- Chains
- 6
- 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
- 20 · best druggability 0.67
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 | 282 | 33% helix, 22% strand | P04818 |
| B, C, D, E, F | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 34% helix, 24% strand | P04818 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, E, F
- BME · Beta-mercaptoethanol · additive · 2 copies · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.67 | 0.79 | 47 | PO4 |
| 2 | 121 | 0.64 | 0.87 | 28 | empty |
| 3 | 405 | 0.64 | 0.78 | 33 | PO4, BME |
| 4 | 418 | 0.63 | 0.77 | 45 | PO4 |
| 5 | 408 | 0.61 | 0.76 | 40 | PO4 |
Interfaces
2 interfaces between chains.
- E–F · 2153 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2071 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2RDA · Human Thymidylate Synthase Stabilized in Active Conformation by R163K Mutation: Asymmetry… · 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 2RDA · PDBe 2RDA · UniProt P04818
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