MolNFT v1 · #118697 · protein
Crystal structure of broadly neutralizing VH1-46 germline-derived CD4- binding site-directed antibody CH235 in complex with HIV-1 clade A/E 93TH057 GP120
5F9W · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of broadly neutralizing VH1-46 germline-derived CD4- binding site-directed antibody CH235…”. X-ray diffraction, 2 ligands (NAG, PO4), 19 pockets (best druggability 0.73). MolNFT…
- PDB
- 5F9W
- Type
- protein
- Length
- 1,544 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; Heavy chain of CH235-lineage antibody CH235; Light…
- UniProt
- A0A0M3KKW9
- Ligands
- NAG, PO4
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 342 | 18% helix, 37% strand | A0A0M3KKW9 |
| B | Heavy chain of CH235-lineage antibody CH235 | protein | 220 | 7% helix, 53% strand | — |
| C, L | Light chain of CH235-lineage antibody CH235 | protein | 210 | 5% helix, 50% strand | — |
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 343 | 18% helix, 37% strand | A0A0M3KKW9 |
| H | Heavy chain of CH235-lineage antibody CH235 | protein | 219 | 7% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, C, G, L
- PO4 · Phosphate ion · ion · 3 copies · chains A, H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.73 | 0.77 | 105 | empty |
| 2 | 829 | 0.69 | 0.76 | 79 | empty |
| 3 | 52 | 0.60 | 0.92 | 20 | empty |
| 4 | 344 | 0.59 | 0.77 | 49 | NAG |
| 5 | 295 | 0.59 | 0.78 | 50 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1797 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1743 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1032 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1017 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 551 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 22 disulfide (N-glycosylation, disulfide).
Compared structures
- 5F9W · Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding… · the same entry in another collection · chain A against A, 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 5F9W · PDBe 5F9W · UniProt A0A0M3KKW9
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