Research workbench
Crystal structure of the non-neutralizing and adcc-potent antibody C11 in complex with HIV-1 clade A/E GP120
Analyse Crystal structure of the non-neutralizing and adcc-potent antibody C11 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OEJ
- Type
- protein
- Length
- 1,526 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; C11 Fab heavy chain; C11 Fab light chain
- UniProt
- A0A0M3KKW9
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 319 | 15% helix, 33% strand | A0A0M3KKW9 |
| H, B | C11 Fab heavy chain | protein | 227 | 4% helix, 41% strand | — |
| L | C11 Fab light chain | protein | 215 | 7% helix, 48% strand | — |
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 322 | 12% helix, 34% strand | A0A0M3KKW9 |
| C | C11 Fab light chain | protein | 216 | 6% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains H, A, B, G, C, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.77 | 0.80 | 96 | NAG |
| 2 | 1114 | 0.77 | 0.79 | 112 | NAG |
| 3 | 70 | 0.75 | 0.98 | 22 | empty |
| 4 | 151 | 0.68 | 0.88 | 22 | empty |
| 5 | 219 | 0.68 | 0.85 | 43 | NAG |
Interfaces
12 interfaces between chains.
- B–C · 1876 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1868 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 678 Ų buried · 6 hydrogen bonds · protein-protein
- G–C · 391 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 6OEJ · Crystal structure of the non-neutralizing and adcc-potent antibody C11 in complex with… · the same entry in another collection · chain G against G, 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 A0A0M3KKW9
- Elsewhere: RCSB PDB 6OEJ · PDBe 6OEJ · UniProt A0A0M3KKW9
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