Research workbench
Ebov gp in complex with variable Fab domains of iggs C4G7 and C13C6
Analyse Ebov gp in complex with variable Fab domains of iggs C4G7 and C13C6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KEN
- Type
- protein
- Length
- 2,147 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ebola surface glycoprotein, GP1; Ebola surface glycoprotein, GP2; C4G7 variable Fab…
- UniProt
- Q05320
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ebola surface glycoprotein, GP1 | protein | 207 | 13% helix, 34% strand | Q05320 |
| B, F, M | Ebola surface glycoprotein, GP2 | protein | 113 | 42% helix, 11% strand | Q05320 |
| C, G, N | C4G7 variable Fab domain heavy chain | protein | 118 | 9% helix, 41% strand | — |
| D, H, O | C4G7 variable Fab domain light chain | protein | 107 | 3% helix, 49% strand | — |
| E, K | Ebola surface glycoprotein, GP1 | protein | 235 | 11% helix, 32% strand | Q05320 |
| I, P | C13C6 variable Fab domain light chain | protein | 107 | 3% helix, 50% strand | — |
| J, Q | C13C6 variable Fab domain heavy chain | protein | 121 | 11% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, F, E, M, K, P, J, Q
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, F, E, M, B, K
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.86 | 0.88 | 81 | empty |
| 2 | 78 | 0.75 | 0.98 | 25 | empty |
| 3 | 154 | 0.72 | 0.91 | 31 | empty |
| 4 | 200 | 0.70 | 0.87 | 34 | empty |
| 5 | 191 | 0.70 | 0.87 | 25 | empty |
Interfaces
35 interfaces between chains.
- K–M · 2455 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2451 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2411 Ų buried · 33 hydrogen bonds · protein-protein
- B–F · 1027 Ų buried · 10 hydrogen bonds · protein-protein
- F–M · 1003 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 8 glycan (disulfide, glycosylation, N-glycosylation).
Compared structures
- 5KEN · EBOV GP in complex with variable Fab domains of IgGs c4G7 and c13C6 · the same entry in another collection · chain E against E, 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 5KEN · PDBe 5KEN · UniProt Q05320
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