Research workbench
Crystal structure of the complex of T.SPIRALIS thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolate
Analyse Crystal structure of the complex of T.SPIRALIS thymidylate synthase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M4Z
- Type
- protein
- Length
- 573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- Q9NDD3
- Ligands
- 7K8
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 287 | 36% helix, 23% strand | Q9NDD3 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 37% helix, 23% strand | Q9NDD3 |
Ligands and binding sites
- 7K8 · [(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.65 | 0.79 | 38 | 7K8 |
| 2 | 414 | 0.61 | 0.76 | 41 | 7K8 |
| 3 | 98 | 0.43 | 0.78 | 23 | GOL |
| 4 | 81 | 0.41 | 0.79 | 19 | empty |
| 5 | 77 | 0.41 | 0.79 | 17 | GOL |
Interfaces
1 interface between chains.
- A–B · 2128 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5M4Z · Crystal structure of the complex of T.spiralis thymidylate synthase with… · 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 Q9NDD3
- Elsewhere: RCSB PDB 5M4Z · PDBe 5M4Z · UniProt Q9NDD3
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