MolNFT v1 · #1834 · protein
E. COLI thymidylate synthase complexed with durd
1BDU: “E. COLI thymidylate synthase complexed with durd”. X-ray diffraction, 2 ligands (DUR, PO4), 2 pockets (best druggability 0.70). MolNFT v1 #1834 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1BDU
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P00470
- Ligands
- DUR, PO4
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 34% helix, 27% strand | P00470 |
Ligands and binding sites
- DUR · 2'-deoxyuridine · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.70 | 0.77 | 53 | PO4, DUR |
| 2 | 66 | 0.29 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 1BDU · E. COLI thymidylate synthase complexed with durd · 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 P00470
- Elsewhere: RCSB PDB 1BDU · PDBe 1BDU · UniProt P00470
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