MolNFT v1 · #138190 · protein
Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 GP120 core
5WB9 · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 GP120…”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 5WB9
- Type
- protein
- Length
- 760 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; N60P23 Fab heavy chain; N60P23 Fab light chain
- UniProt
- A0A0M3KKW9
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 340 | 17% helix, 34% strand | A0A0M3KKW9 |
| H | N60P23 Fab heavy chain | protein | 220 | 8% helix, 50% strand | — |
| L | N60P23 Fab light chain | protein | 200 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains G
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.78 | 0.84 | 75 | MPD |
| 2 | 537 | 0.61 | 0.74 | 55 | empty |
| 3 | 133 | 0.46 | 0.78 | 24 | empty |
| 4 | 177 | 0.46 | 0.75 | 32 | empty |
| 5 | 76 | 0.45 | 0.81 | 16 | NAG |
Interfaces
3 interfaces between chains.
- H–L · 1703 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 779 Ų buried · 15 hydrogen bonds · protein-protein
- G–L · 277 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5WB9 · Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E… · 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 5WB9 · PDBe 5WB9 · UniProt A0A0M3KKW9
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