Research workbench
Crystal structure of C.ELEGANS thymidylate synthase in complex with an inhibitor N(4)OHDCMP
Analyse Crystal structure of C.ELEGANS thymidylate synthase in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PSG
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- Q9Y052
- Ligands
- NOH
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 289 | 34% helix, 22% strand | Q9Y052 |
Ligands and binding sites
- NOH · 2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.62 | 0.78 | 25 | NOH |
| 2 | 403 | 0.62 | 0.77 | 33 | NOH |
| 3 | 125 | 0.44 | 0.77 | 21 | empty |
| 4 | 101 | 0.41 | 0.78 | 21 | empty |
| 5 | 88 | 0.41 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1926 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4PSG · Crystal Structure of C.elegans Thymidylate Synthase in complex with an inhibitor… · 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 Q9Y052
- Elsewhere: RCSB PDB 4PSG · PDBe 4PSG · UniProt Q9Y052
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