MolNFT v1 · #134744 · protein
Crystal structure of broadly neutralizing VRC01-class antibody N6 in complex with HIV-1 clade G strain X2088 GP120 core
5TE4: “Crystal structure of broadly neutralizing VRC01-class antibody N6 in complex with HIV-1 clade G strain X2088…”. X-ray diffraction, 2 ligands (NAG, SO4), 10 pockets (best druggability 0.74). MolNFT v1 #134744 on GenesisL1: 3D…
- PDB
- 5TE4
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade G strain X2088 GP120; Heavy chain of antibody N6; Light chain of antibody N6
- Ligands
- NAG, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 clade G strain X2088 GP120 | protein | 341 | 17% helix, 36% strand | — |
| H | Heavy chain of antibody N6 | protein | 224 | 9% helix, 51% strand | — |
| L | Light chain of antibody N6 | protein | 210 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains G, L
- SO4 · Sulfate ion · ion · 8 copies · chains G, H, L
- BU3 · (R,R)-2,3-butanediol · additive · chains G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.74 | 0.83 | 52 | empty |
| 2 | 62 | 0.71 | 0.97 | 19 | BU3 |
| 3 | 81 | 0.55 | 0.86 | 19 | NAG |
| 4 | 111 | 0.54 | 0.83 | 21 | empty |
| 5 | 319 | 0.52 | 0.73 | 47 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1804 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 962 Ų buried · 22 hydrogen bonds · protein-protein
- G–L · 350 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 11 disulfide (N-glycosylation, disulfide).
Compared structures
- 5TE4 · Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1… · the same entry in another collection · chain H against H, 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 5TE4 · PDBe 5TE4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.