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Crystal structure of epstein-barr virus (EBV) ghgl and in complex with the ligand binding domian (lbd) of EPHA2
Analyse Crystal structure of epstein-barr virus (EBV) ghgl and in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZE
- Type
- protein
- Length
- 3,716 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Ephrin type-a receptor 2
- EC
- 2.7.10.1
- UniProt
- P03231, P03212, P29317
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Envelope glycoprotein H | protein | 655 | 36% helix, 20% strand | P03231 |
| B, D, F, H | Envelope glycoprotein L | protein | 109 | 28% helix, 17% strand | P03212 |
| I, J, K, L | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 165 | 2% helix, 49% strand | P29317 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
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 | 268 | 0.75 | 0.88 | 36 | empty |
| 2 | 256 | 0.74 | 0.87 | 37 | empty |
| 3 | 252 | 0.73 | 0.87 | 37 | empty |
| 4 | 309 | 0.71 | 0.84 | 45 | empty |
| 5 | 546 | 0.70 | 0.79 | 64 | empty |
Interfaces
17 interfaces between chains.
- G–H · 2293 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2288 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2279 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2274 Ų buried · 25 hydrogen bonds · protein-protein
- D–J · 938 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 7CZE · Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding… · the same entry in another collection · chain L against L, 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 P03231
- Every structure of UniProt P03212
- Every structure of UniProt P29317
- Elsewhere: RCSB PDB 7CZE · PDBe 7CZE · UniProt P03231 · UniProt P03212 · UniProt P29317
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