Research workbench
Human herpesvirus-8 GH/GL in complex with EPHA2
Analyse Human herpesvirus-8 GH/GL in complex with EPHA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B7N
- Type
- protein
- Length
- 905 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Envelope glycoprotein H; Envelope glycoprotein L
- EC
- 2.7.10.1
- UniProt
- P29317, Q98142, Q76RG7
- Ligands
- NAG, NA, CL
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 158 | 6% helix, 49% strand | P29317 |
| H | Envelope glycoprotein H | protein | 637 | 40% helix, 19% strand | Q98142 |
| L | Envelope glycoprotein L | protein | 110 | 44% helix, 18% strand | Q76RG7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains H, L
- NA · Sodium ion · metal · 10 copies · chains E, L, H
- CL · Chloride ion · ion · 4 copies · chains E, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.65 | 0.91 | 21 | empty |
| 2 | 289 | 0.64 | 0.80 | 44 | empty |
| 3 | 197 | 0.56 | 0.80 | 25 | empty |
| 4 | 105 | 0.51 | 0.82 | 23 | empty |
| 5 | 166 | 0.50 | 0.77 | 42 | CL |
Interfaces
3 interfaces between chains.
- H–L · 2511 Ų buried · 28 hydrogen bonds · protein-protein
- E–L · 904 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 140 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 P29317
- Every structure of UniProt Q98142
- Every structure of UniProt Q76RG7
- Elsewhere: RCSB PDB 7B7N · PDBe 7B7N · UniProt P29317 · UniProt Q98142 · UniProt Q76RG7
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