Research workbench
Crystal structure of broadly and potently neutralizing antibody vrc- CH31 in complex with HIV-1 clade A/E stran 93TH057 GP120 with loop D and loop V5 from clade a strain KER_2018_11
Analyse Crystal structure of broadly and potently neutralizing antibody vrc- CH31 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LSR
- Type
- protein
- Length
- 770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120 with loop D and V5 from strain KER_2018_11; Heavy chain of…
- Ligands
- NAG, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 with loop D and V5 from strain KER_2018_11 | protein | 345 | 17% helix, 37% strand | — |
| H | Heavy chain of antibody vrc-CH31 | protein | 217 | 6% helix, 48% strand | — |
| L | Light chain of antibody vrc-CH31 (N70D mutation) | protein | 208 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains G, L
- SO4 · Sulfate ion · ion · 5 copies · chains G, H
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 | 808 | 0.77 | 0.81 | 95 | empty |
| 2 | 414 | 0.58 | 0.75 | 53 | empty |
| 3 | 122 | 0.54 | 0.83 | 29 | NAG |
| 4 | 58 | 0.52 | 0.87 | 19 | NAG |
| 5 | 87 | 0.42 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1644 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 824 Ų buried · 13 hydrogen bonds · protein-protein
- G–L · 485 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4LSR · Crystal structure of broadly and potently neutralizing antibody VRC-CH31 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 4LSR · PDBe 4LSR
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