MolNFT v1 · #118672 · protein
Crystal structure of broadly neutralizing VH1-46 germline-derived CD4- binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 GP120
5F96 · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of broadly neutralizing VH1-46 germline-derived CD4- binding site-directed antibody…”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.65). MolNFT v1 #118672…
- PDB
- 5F96
- Type
- protein
- Length
- 770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; Heavy chain of antibody CH235.12; Light chain of…
- UniProt
- A0A0M3KKW9
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 339 | 19% helix, 37% strand | A0A0M3KKW9 |
| H | Heavy chain of antibody CH235.12 | protein | 220 | 8% helix, 55% strand | — |
| L | Light chain of antibody CH235.12 | protein | 211 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains G, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.65 | 0.82 | 38 | empty |
| 2 | 516 | 0.59 | 0.73 | 51 | empty |
| 3 | 61 | 0.53 | 0.87 | 18 | NAG |
| 4 | 69 | 0.50 | 0.85 | 22 | empty |
| 5 | 50 | 0.49 | 0.87 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1662 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 958 Ų buried · 18 hydrogen bonds · protein-protein
- G–L · 337 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5F96 · Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding… · 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
- Every structure of UniProt A0A0M3KKW9
- Elsewhere: RCSB PDB 5F96 · PDBe 5F96 · UniProt A0A0M3KKW9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.