MolNFT v1 · #124418 · protein
Ebov gp in complex with variable Fab domains of iggs C4G7 and C13C6
5KEN · Ebola surface glycoprotein, GP1: “Ebov gp in complex with variable Fab domains of iggs C4G7 and C13C6”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #124418 on GenesisL1: 3D…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.