Research workbench
Crystal structure of broadly neutralizing VH1-46 germline-derived CD4- binding site-directed antibody CH235.09 in complex with HIV-1 clade A/E 93TH057 GP120
Analyse Crystal structure of broadly neutralizing VH1-46 germline-derived CD4- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9O
- Type
- protein
- Length
- 771 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; CH235.9 heavy chain; CH235.09 light chain
- UniProt
- A0A0M3KKW9
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.71
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 | 341 | 18% helix, 38% strand | A0A0M3KKW9 |
| H | CH235.9 heavy chain | protein | 220 | 10% helix, 54% strand | — |
| L | CH235.09 light chain | protein | 210 | 6% helix, 50% 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 · 2 copies · chains G
- 15P · Polyethylene glycol (N=34) · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.71 | 0.84 | 62 | empty |
| 2 | 279 | 0.56 | 0.77 | 43 | NAG |
| 3 | 73 | 0.49 | 0.83 | 18 | NAG |
| 4 | 211 | 0.42 | 0.72 | 29 | empty |
| 5 | 72 | 0.31 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1736 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 860 Ų buried · 18 hydrogen bonds · protein-protein
- G–L · 357 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5F9O · 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 5F9O · PDBe 5F9O · UniProt A0A0M3KKW9
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