Research workbench
Crystal structure of kshv ORF68
Analyse Crystal structure of kshv ORF68 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XF9
- Type
- protein
- Length
- 2,124 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Packaging protein UL32
- UniProt
- P88958
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 56% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Packaging protein UL32 | protein | 425 | 56% helix, 4% strand | P88958 |
| B | Packaging protein UL32 | protein | 424 | 57% helix, 3% strand | P88958 |
| C | Packaging protein UL32 | protein | 424 | 57% helix, 4% strand | P88958 |
| D | Packaging protein UL32 | protein | 426 | 55% helix, 4% strand | P88958 |
| E | Packaging protein UL32 | protein | 425 | 56% helix, 4% strand | P88958 |
Ligands and binding sites
- ZN · Zinc ion · metal · 15 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.73 | 0.78 | 110 | empty |
| 2 | 50 | 0.71 | 0.99 | 18 | empty |
| 3 | 52 | 0.71 | 0.98 | 17 | empty |
| 4 | 54 | 0.70 | 0.98 | 19 | empty |
| 5 | 547 | 0.68 | 0.78 | 65 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1266 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1263 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1261 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1261 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1211 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6XF9 · Crystal structure of KSHV ORF68 · 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 P88958
- Elsewhere: RCSB PDB 6XF9 · PDBe 6XF9 · UniProt P88958
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.