Research workbench
Crystal structure of broadly and potently neutralizing antibody vrc- CH31 in complex with HIV-1 clade A/E GP120 93TH057 with loop D and loop V5 from clade a strain 3415_V1_C1
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
- 4LSQ
- Type
- protein
- Length
- 775 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 3415_V1_C1; Heavy chain of…
- Ligands
- NAG, CD, NA, CL
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 with loop D and V5 from strain 3415_V1_C1 | protein | 344 | 16% helix, 37% strand | — |
| H | Heavy chain of antibody vrc-CH31 | protein | 222 | 5% helix, 47% strand | — |
| L | Light chain of antibody vrc-CH31 with N70D mutation | protein | 209 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains G, L
- CD · Cadmium ion · metal · 5 copies · chains G, H, L
- NA · Sodium ion · metal · 4 copies · chains G, H
- CL · Chloride ion · ion · 3 copies · chains G, H
- BU3 · (R,R)-2,3-butanediol · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.77 | 0.81 | 83 | BU3, NA, CD, CL |
| 2 | 213 | 0.59 | 0.81 | 33 | NAG |
| 3 | 397 | 0.58 | 0.75 | 51 | empty |
| 4 | 68 | 0.57 | 0.88 | 19 | NAG |
| 5 | 235 | 0.56 | 0.78 | 29 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1731 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 708 Ų buried · 16 hydrogen bonds · protein-protein
- G–L · 345 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4LSQ · 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 4LSQ · PDBe 4LSQ
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