Research workbench
KAPOSI'S sarcoma-associated herpesvirus (kshv), C12 portal dodecamer structure
Analyse KAPOSI'S sarcoma-associated herpesvirus (kshv), C12 portal dodecamer structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PPI
- Type
- protein
- Length
- 4,956 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Portal protein
- UniProt
- Q76RH0
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Portal protein | protein | 413 | 53% helix, 9% strand | Q76RH0 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.85 | 0.88 | 63 | empty |
| 2 | 868 | 0.84 | 0.86 | 72 | empty |
| 3 | 954 | 0.83 | 0.85 | 86 | empty |
| 4 | 969 | 0.83 | 0.84 | 88 | empty |
| 5 | 954 | 0.83 | 0.84 | 85 | empty |
Interfaces
24 interfaces between chains.
- C–D · 4044 Ų buried · 30 hydrogen bonds · protein-protein
- A–L · 4044 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 4039 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 4036 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 4036 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6PPI · Kaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodecamer structure · 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 Q76RH0
- Elsewhere: RCSB PDB 6PPI · PDBe 6PPI · UniProt Q76RH0
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