Research workbench
Kshv lana (ORF73) C-terminal domain, decameric ring: orthorhombic crystal form
Analyse Kshv lana (ORF73) C-terminal domain, decameric ring: orthorhombic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YPZ
- Type
- protein
- Length
- 1,347 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kshv lana
- UniProt
- Q76SB0
- Pockets
- 20 · best druggability 0.53
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, G, I, J | Kshv lana | protein | 135 | 33% helix, 22% strand | Q76SB0 |
| B | Kshv lana | protein | 134 | 31% helix, 25% strand | Q76SB0 |
| E | Kshv lana | protein | 133 | 33% helix, 20% strand | Q76SB0 |
| F | Kshv lana | protein | 137 | 30% helix, 21% strand | Q76SB0 |
| H | Kshv lana | protein | 133 | 35% helix, 24% strand | Q76SB0 |
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.53 | 0.80 | 23 | empty |
| 2 | 152 | 0.53 | 0.80 | 25 | empty |
| 3 | 147 | 0.50 | 0.78 | 23 | empty |
| 4 | 136 | 0.49 | 0.79 | 25 | empty |
| 5 | 111 | 0.47 | 0.79 | 21 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2276 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2185 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 2146 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2136 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2004 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2YPZ · KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic crystal form · the same entry in another collection · chain C against C, 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 Q76SB0
- Elsewhere: RCSB PDB 2YPZ · PDBe 2YPZ · UniProt Q76SB0
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