MolNFT v1 · #124417 · protein
Ebov sgp in complex with variable Fab domains of iggs C13C6 and BDBV91
5KEM · BDBV91 variable Fab domain light chain: “Ebov sgp in complex with variable Fab domains of iggs C13C6 and BDBV91”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #124417 on GenesisL1: 3D structure, binding sites…
- 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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