MolNFT v1 · #120531 · protein
Structural analysis of kshv thymidylate synthase
5H38 · ORF70: “Structural analysis of kshv thymidylate synthase”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.70). MolNFT v1 #120531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H38
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF70
- UniProt
- F5HBQ9
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF70 | protein | 283 | 35% helix, 24% strand | F5HBQ9 |
| B | ORF70 | protein | 284 | 35% helix, 24% strand | F5HBQ9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.70 | 0.79 | 51 | PO4 |
| 2 | 506 | 0.68 | 0.78 | 44 | PO4 |
| 3 | 129 | 0.43 | 0.76 | 25 | empty |
| 4 | 107 | 0.38 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2135 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5H38 · Structural analysis of KSHV thymidylate synthase · 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 F5HBQ9
- Elsewhere: RCSB PDB 5H38 · PDBe 5H38 · UniProt F5HBQ9
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