MolNFT v1 · #134747 · protein
Crystal structure of broadly neutralizing VRC01-class antibody N6 in complex with HIV-1 clade C strain DU172.17 GP120 core
5TE7 · Heavy chain of N6: “Crystal structure of broadly neutralizing VRC01-class antibody N6 in complex with HIV-1 clade C strain…”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.77). MolNFT v1 #134747 on GenesisL1: 3D…
- PDB
- 5TE7
- Type
- protein
- Length
- 771 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of N6; Light chain of N6; HIV-1 GP120 core
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of N6 | protein | 225 | 8% helix, 50% strand | — |
| L | Light chain of N6 | protein | 210 | 6% helix, 50% strand | — |
| G | HIV-1 GP120 core | protein | 336 | 18% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains L, G
- EDO · 1,2-ethanediol · additive · 7 copies · chains H, L, G
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.77 | 0.85 | 62 | EDO |
| 2 | 345 | 0.61 | 0.78 | 45 | EDO |
| 3 | 262 | 0.59 | 0.79 | 36 | EDO |
| 4 | 369 | 0.55 | 0.74 | 46 | empty |
| 5 | 66 | 0.54 | 0.87 | 17 | NAG |
Interfaces
3 interfaces between chains.
- H–L · 1867 Ų buried · 18 hydrogen bonds · protein-protein
- H–G · 967 Ų buried · 26 hydrogen bonds · protein-protein
- L–G · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5TE7 · 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 5TE7 · PDBe 5TE7
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