MolNFT v1 · #186477 · protein
Crystal structure of broadly neutralizing antibody MAB1382 in complex with hepatitis C virus envelope glycoprotein E2 ectodomain
7RFC · MAB1382 heavy chain: “Crystal structure of broadly neutralizing antibody MAB1382 in complex with hepatitis C virus envelope…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 14 pockets (best druggability 0.60). MolNFT v1 #186477 on…
- PDB
- 7RFC
- Type
- protein
- Length
- 1,304 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAB1382 heavy chain; MAB1382 light chain; Envelope glycoprotein E2
- UniProt
- A0A2P0NE26
- Ligands
- NAG, BMA, MAN
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAB1382 heavy chain | protein | 221 | 7% helix, 52% strand | — |
| B | MAB1382 light chain | protein | 215 | 4% helix, 54% strand | — |
| C | Envelope glycoprotein E2 | protein | 211 | 16% helix, 29% strand | A0A2P0NE26 |
| D | Envelope glycoprotein E2 | protein | 223 | 13% helix, 28% strand | A0A2P0NE26 |
| H | MAB1382 heavy chain | protein | 220 | 7% helix, 51% strand | — |
| L | MAB1382 light chain | protein | 214 | 5% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.60 | 0.76 | 40 | empty |
| 2 | 456 | 0.60 | 0.75 | 47 | empty |
| 3 | 413 | 0.56 | 0.74 | 56 | empty |
| 4 | 221 | 0.53 | 0.77 | 28 | empty |
| 5 | 132 | 0.47 | 0.78 | 17 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1898 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 891 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 887 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 485 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 7RFC · Crystal structure of broadly neutralizing antibody mAb1382 in complex with Hepatitis C… · 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 A0A2P0NE26
- Elsewhere: RCSB PDB 7RFC · PDBe 7RFC · UniProt A0A2P0NE26
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