Research workbench
Crystal structure of EBV GH/GL bound with neutralizing antibody 1D8
Analyse Crystal structure of EBV GH/GL bound with neutralizing antibody 1D8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D5Z
- Type
- protein
- Length
- 4,704 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Light chain of 1D8; Heavy chain of 1D8
- UniProt
- Q3KSQ3, Q3KSS3
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, A, E, I | Envelope glycoprotein H | protein | 655 | 38% helix, 21% strand | Q3KSQ3 |
| N, B, F, J | Envelope glycoprotein L | protein | 94 | 30% helix, 15% strand | Q3KSS3 |
| O, C, G, K | Light chain of 1D8 | protein | 213 | 6% helix, 52% strand | — |
| P, D, H, L | Heavy chain of 1D8 | protein | 214 | 6% helix, 50% strand | — |
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 | 188 | 0.83 | 0.97 | 26 | empty |
| 2 | 191 | 0.82 | 0.97 | 26 | empty |
| 3 | 1144 | 0.74 | 0.77 | 105 | empty |
| 4 | 80 | 0.73 | 0.96 | 18 | empty |
| 5 | 78 | 0.73 | 0.96 | 20 | empty |
Interfaces
32 interfaces between chains.
- I–J · 2245 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2234 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2227 Ų buried · 24 hydrogen bonds · protein-protein
- M–N · 2211 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1788 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide (disulfide).
Compared structures
- 7D5Z · Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8 · the same entry in another collection · chain M against M, 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 Q3KSQ3
- Every structure of UniProt Q3KSS3
- Elsewhere: RCSB PDB 7D5Z · PDBe 7D5Z · UniProt Q3KSQ3 · UniProt Q3KSS3
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