Research workbench
Ebov sgp in complex with variable Fab domains of iggs C13C6 and BDBV91
Analyse Ebov sgp in complex with variable Fab domains of iggs C13C6 and BDBV91 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KEM
- Type
- protein
- Length
- 1,376 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BDBV91 variable Fab domain light chain; BDBV91 variable Fab domain heavy chain; C13C6…
- UniProt
- Q05320
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, H | BDBV91 variable Fab domain light chain | protein | 107 | 4% helix, 44% strand | — |
| B, G | BDBV91 variable Fab domain heavy chain | protein | 121 | 3% helix, 32% strand | — |
| D, I | C13C6 variable Fab domain heavy chain | protein | 121 | 7% helix, 36% strand | — |
| E, J | C13C6 variable Fab domain light chain | protein | 107 | 3% helix, 48% strand | — |
| A, F | Ebola secreted glycoprotein | protein | 232 | 13% helix, 28% strand | Q05320 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.84 | 0.85 | 154 | empty |
| 2 | 65 | 0.74 | 0.98 | 21 | empty |
| 3 | 69 | 0.72 | 0.97 | 22 | empty |
| 4 | 61 | 0.72 | 0.97 | 23 | empty |
| 5 | 62 | 0.72 | 0.97 | 22 | empty |
Interfaces
17 interfaces between chains.
- A–F · 836 Ų buried · 10 hydrogen bonds · protein-protein
- H–G · 679 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 677 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 652 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 649 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5KEM · EBOV sGP in complex with variable Fab domains of IgGs c13C6 and BDBV91 · the same entry in another collection · chain F against F, 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 Q05320
- Elsewhere: RCSB PDB 5KEM · PDBe 5KEM · UniProt Q05320
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