MolNFT v1 · #183636 · protein
Structure of the pentameric C-terminal domain of the capsid protein from KAPOSI'S sarcoma-associated herpesvirus (kshv)
7NXQ · Capsid vertex component 2: “Structure of the pentameric C-terminal domain of the capsid protein from KAPOSI'S sarcoma-associated…”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #183636 on GenesisL1: 3D…
- PDB
- 7NXQ
- Type
- protein
- Length
- 4,056 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid vertex component 2
- UniProt
- Q76RI7
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 10 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid vertex component 2 | protein | 412 | 54% helix, 5% strand | Q76RI7 |
| B | Capsid vertex component 2 | protein | 404 | 55% helix, 5% strand | Q76RI7 |
| C | Capsid vertex component 2 | protein | 411 | 55% helix, 5% strand | Q76RI7 |
| D | Capsid vertex component 2 | protein | 404 | 55% helix, 5% strand | Q76RI7 |
| E | Capsid vertex component 2 | protein | 406 | 55% helix, 5% strand | Q76RI7 |
| F | Capsid vertex component 2 | protein | 405 | 55% helix, 5% strand | Q76RI7 |
| G | Capsid vertex component 2 | protein | 405 | 55% helix, 5% strand | Q76RI7 |
| H | Capsid vertex component 2 | protein | 403 | 56% helix, 5% strand | Q76RI7 |
| I | Capsid vertex component 2 | protein | 404 | 55% helix, 5% strand | Q76RI7 |
| J | Capsid vertex component 2 | protein | 402 | 55% helix, 6% strand | Q76RI7 |
Ligands and binding sites
- ACT · Acetate ion · additive · 20 copies · chains A, E, D, B, I, C, F, G, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1041 | 0.81 | 0.82 | 97 | empty |
| 2 | 801 | 0.75 | 0.79 | 98 | empty |
| 3 | 787 | 0.69 | 0.76 | 65 | empty |
| 4 | 611 | 0.67 | 0.77 | 66 | ACT |
| 5 | 315 | 0.62 | 0.79 | 55 | ACT |
Interfaces
17 interfaces between chains.
- A–D · 1272 Ų buried · 16 hydrogen bonds · protein-protein
- B–I · 1202 Ų buried · 19 hydrogen bonds · protein-protein
- F–I · 1194 Ų buried · 17 hydrogen bonds · protein-protein
- B–G · 1192 Ų buried · 18 hydrogen bonds · protein-protein
- E–J · 1170 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7NXQ · Structure of the pentameric C-terminal domain of the capsid protein from Kaposi's… · 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 Q76RI7
- Elsewhere: RCSB PDB 7NXQ · PDBe 7NXQ · UniProt Q76RI7
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