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Crystal structure of an immature VRC01-class antibody DRVIA7 from a chinese donor bound to clade A/E HIV-1 GP120 core
Analyse Crystal structure of an immature VRC01-class antibody DRVIA7 from a chinese… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CD5
- Type
- protein
- Length
- 770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 93TH057 HIV-1 GP120 core; DRVIA7 Fab heavy chain; DRVIA7 Fab light chain
- Ligands
- NAG, BMA, MAN
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 93TH057 HIV-1 GP120 core | protein | 343 | 16% helix, 37% strand | — |
| C | DRVIA7 Fab heavy chain | protein | 220 | 7% helix, 50% strand | — |
| D | DRVIA7 Fab light chain | protein | 207 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.70 | 0.83 | 44 | empty |
| 2 | 503 | 0.62 | 0.75 | 54 | empty |
| 3 | 152 | 0.61 | 0.84 | 27 | empty |
| 4 | 64 | 0.58 | 0.90 | 21 | NAG |
| 5 | 153 | 0.50 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1841 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 835 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 342 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5CD5 · Crystal structure of an immature VRC01-class antibody DRVIA7 from a Chinese donor bound… · 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
- Elsewhere: RCSB PDB 5CD5 · PDBe 5CD5
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