MolNFT v1 · #99075 · protein
Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade a strain KER_2018_11 GP120
4LSS · Envelope glycoprotein GP120: “Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade a strain…”. X-ray diffraction, 2 ligands (NAG, NA), 9 pockets (best druggability 0.74). MolNFT v1 #99075…
- PDB
- 4LSS
- Type
- protein
- Length
- 767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Heavy chain of antibody VRC01; Light chain of antibody VRC01…
- Ligands
- NAG, NA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 | protein | 335 | 17% helix, 38% strand | — |
| H | Heavy chain of antibody VRC01 | protein | 224 | 8% helix, 52% strand | — |
| L | Light chain of antibody VRC01 with N72T mutation | protein | 208 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains G, L
- NA · Sodium ion · metal · 3 copies · chains G, H, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains G, H
- IPA · Isopropyl alcohol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.74 | 0.87 | 46 | empty |
| 2 | 176 | 0.72 | 0.89 | 34 | IPA |
| 3 | 134 | 0.54 | 0.81 | 19 | empty |
| 4 | 90 | 0.48 | 0.82 | 19 | NAG |
| 5 | 173 | 0.48 | 0.76 | 33 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1842 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1062 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 259 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4LSS · Crystal structure of broadly and potently neutralizing antibody VRC01 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 4LSS · PDBe 4LSS
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