Research workbench
Crystal structure of an HIV-1 GP120 engineered outer domain with a MAN9 glycan at position N276, in complex with broadly neutralizing antibody VRC01
Analyse Crystal structure of an HIV-1 GP120 engineered outer domain with a MAN9 glycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KZC
- Type
- protein
- Length
- 1,759 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC01 Fab heavy chain; Engineered outer domain of GP120; VRC01 Fab light chain
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, B, E | VRC01 Fab heavy chain | protein | 214 | 7% helix, 50% strand | — |
| A | Engineered outer domain of GP120 | protein | 170 | 19% helix, 36% strand | — |
| L, G | VRC01 Fab light chain | protein | 206 | 7% helix, 52% strand | — |
| C | Engineered outer domain of GP120 | protein | 170 | 19% helix, 36% strand | — |
| D | VRC01 Fab light chain | protein | 209 | 4% helix, 46% strand | — |
| F | Engineered outer domain of GP120 | protein | 156 | 18% helix, 31% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains L, B, D, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, L, C, D, F, G
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains L, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.76 | 0.98 | 25 | empty |
| 2 | 844 | 0.71 | 0.77 | 101 | empty |
| 3 | 280 | 0.69 | 0.84 | 38 | NAG |
| 4 | 122 | 0.60 | 0.86 | 27 | empty |
| 5 | 134 | 0.56 | 0.83 | 23 | empty |
Interfaces
12 interfaces between chains.
- E–G · 1745 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1734 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1665 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1035 Ų buried · 24 hydrogen bonds · protein-protein
- H–A · 935 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5KZC · Crystal structure of an HIV-1 gp120 engineered outer domain with a Man9 glycan at… · the same entry in another collection · chain H against H, 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 5KZC · PDBe 5KZC
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