MolNFT v1 · #147346 · protein
Structure of bdbv gpcl in complex with the pan-ebolavirus mab adi- 15878
6EA5 · Envelope glycoprotein: “Structure of bdbv gpcl in complex with the pan-ebolavirus mab adi- 15878”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.90). MolNFT v1 #147346 on GenesisL1: 3D structure…
- PDB
- 6EA5
- Type
- protein
- Length
- 2,071 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; Glycoprotein; Adi-15878 Fab heavy chain; Adi-15878 Fab light chain
- UniProt
- B8XCN0, R4QRC0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 11 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein | protein | 162 | 9% helix, 42% strand | B8XCN0 |
| B, D | Glycoprotein | protein | 104 | 37% helix, 14% strand | R4QRC0 |
| C | Envelope glycoprotein | protein | 158 | 9% helix, 38% strand | B8XCN0 |
| E | Envelope glycoprotein | protein | 155 | 7% helix, 43% strand | B8XCN0 |
| F | Glycoprotein | protein | 103 | 37% helix, 14% strand | R4QRC0 |
| H | Adi-15878 Fab heavy chain | protein | 213 | 3% helix, 49% strand | — |
| L | Adi-15878 Fab light chain | protein | 210 | 6% helix, 44% strand | — |
| M | Adi-15878 Fab heavy chain | protein | 217 | 3% helix, 47% strand | — |
| N | Adi-15878 Fab light chain | protein | 212 | 7% helix, 44% strand | — |
| Q | Adi-15878 Fab heavy chain | protein | 222 | 5% helix, 44% strand | — |
| R | Adi-15878 Fab light chain | protein | 211 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains E, F, C, D, M, A, B, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains E, C, M
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains M, N
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 | 990 | 0.90 | 0.91 | 126 | empty |
| 2 | 503 | 0.77 | 0.84 | 45 | empty |
| 3 | 70 | 0.75 | 0.99 | 22 | empty |
| 4 | 670 | 0.73 | 0.80 | 87 | empty |
| 5 | 137 | 0.71 | 0.91 | 30 | empty |
Interfaces
29 interfaces between chains.
- A–B · 2498 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2378 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2358 Ų buried · 22 hydrogen bonds · protein-protein
- Q–R · 1783 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1734 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6EA5 · Structure of BDBV GPcl in complex with the pan-ebolavirus mAb ADI-15878 · 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
- Every structure of UniProt R4QRC0
- Elsewhere: RCSB PDB 6EA5 · PDBe 6EA5 · UniProt B8XCN0 · UniProt R4QRC0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.