Research workbench
Crystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D- 001739, in complex with clade A/E HIV-1 GP120 core
Analyse Crystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D- 001739, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S1Q
- Type
- protein
- Length
- 781 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 GP120 core; Fab of VRC01-lineage ANTIBODY,45-VRC01.H03+06.D-001739 heavy chain; Fab…
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 GP120 core | protein | 344 | 19% helix, 37% strand | — |
| H | Fab of VRC01-lineage ANTIBODY,45-VRC01.H03+06.D-001739 heavy chain | protein | 228 | 7% helix, 51% strand | — |
| L | Fab of VRC01 light chain | protein | 209 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.71 | 0.80 | 63 | NAG |
| 2 | 53 | 0.57 | 0.90 | 18 | empty |
| 3 | 66 | 0.54 | 0.87 | 15 | NAG |
| 4 | 83 | 0.48 | 0.82 | 19 | empty |
| 5 | 56 | 0.45 | 0.84 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1702 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1201 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 305 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4S1Q · Crystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D-001739, 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
- Elsewhere: RCSB PDB 4S1Q · PDBe 4S1Q
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