Research workbench
Crystal structure of a VRC01-lineage antibody, 45-VRC01.H5.F-185917, in complex with clade A/E HIV-1 GP120 core
Analyse Crystal structure of a VRC01-lineage antibody, 45-VRC01.H5.F-185917, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S1S
- Type
- protein
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; Fab of VRC01-lineage ANTIBODY,45-VRC01.H5.F-185917…
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.67
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 | 342 | 17% helix, 37% strand | — |
| H | Fab of VRC01-lineage ANTIBODY,45-VRC01.H5.F-185917 heavy chain | protein | 228 | 3% helix, 44% strand | — |
| L | Fab of VRC01 light chain | protein | 208 | 2% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.67 | 0.86 | 41 | empty |
| 2 | 237 | 0.60 | 0.80 | 35 | empty |
| 3 | 164 | 0.55 | 0.81 | 31 | empty |
| 4 | 63 | 0.53 | 0.87 | 16 | NAG |
| 5 | 231 | 0.49 | 0.75 | 39 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1766 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1066 Ų buried · 14 hydrogen bonds · protein-protein
- G–L · 245 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4S1S · Crystal structure of a VRC01-lineage antibody, 45-VRC01.H5.F-185917, 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 4S1S · PDBe 4S1S
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