Research workbench
BDBV223 Fab bound to synthetic peptide of bundibugyo virus glycoprotein stalk
Analyse BDBV223 Fab bound to synthetic peptide of bundibugyo virus glycoprotein stalk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7J
- Type
- protein
- Length
- 900 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BDBV223 antibody heavy chain; BDBV223 antibody light chain; Envelope glycoprotein
- UniProt
- B8XCN0
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BDBV223 antibody heavy chain | protein | 223 | 5% helix, 48% strand | — |
| H | BDBV223 antibody heavy chain | protein | 219 | 4% helix, 47% strand | — |
| B, L | BDBV223 antibody light chain | protein | 214 | 6% helix, 50% strand | — |
| C, D | Envelope glycoprotein | protein | 15 | 47% helix, 0% strand | B8XCN0 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.60 | 0.76 | 45 | empty |
| 2 | 397 | 0.60 | 0.76 | 42 | empty |
| 3 | 173 | 0.45 | 0.75 | 24 | empty |
| 4 | 90 | 0.42 | 0.79 | 16 | empty |
| 5 | 122 | 0.41 | 0.76 | 30 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1842 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1840 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 621 Ų buried · 9 hydrogen bonds · protein-protein
- H–C · 591 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 217 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6N7J · BDBV223 Fab bound to synthetic peptide of Bundibugyo virus Glycoprotein Stalk · 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 B8XCN0
- Elsewhere: RCSB PDB 6N7J · PDBe 6N7J · UniProt B8XCN0
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