Research workbench
Crystal structure of the RV144 C1-C2 specific antibody CH55 Fab in complex with HIV-1 clade A/E GP120
Analyse Crystal structure of the RV144 C1-C2 specific antibody CH55 Fab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFI
- Type
- protein
- Length
- 739 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; CH55 Fab heavy chain; CH55 Fab light chain
- UniProt
- A0A0M3KKW9
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 312 | 15% helix, 36% strand | A0A0M3KKW9 |
| H | CH55 Fab heavy chain | protein | 214 | 4% helix, 50% strand | — |
| L | CH55 Fab light chain | protein | 213 | 5% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.64 | 0.74 | 70 | empty |
| 2 | 51 | 0.59 | 0.91 | 13 | empty |
| 3 | 75 | 0.49 | 0.84 | 20 | NAG |
| 4 | 110 | 0.45 | 0.78 | 13 | empty |
| 5 | 173 | 0.45 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1744 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 570 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 484 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6OFI · CRYSTAL STRUCTURE OF the RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB IN COMPLEX WITH HIV-1… · 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 6OFI · PDBe 6OFI · UniProt A0A0M3KKW9
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