MolNFT v1 · #80128 · protein
Crystal structure of A32 Fab, an adcc mediating anti-HIV-1 antibody
3TNM · Fab heavy chain of human anti-HIV-1 env antibody A32: “Crystal structure of A32 Fab, an adcc mediating anti-HIV-1 antibody”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.70). MolNFT v1 #80128 on GenesisL1: 3D…
- PDB
- 3TNM
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain of human anti-HIV-1 env antibody A32; Fab light chain of human anti-HIV-1…
- Ligands
- CL
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain of human anti-HIV-1 env antibody A32 | protein | 221 | 7% helix, 52% strand | — |
| L, B | Fab light chain of human anti-HIV-1 env antibody A32 | protein | 210 | 6% helix, 52% strand | — |
| A | Fab heavy chain of human anti-HIV-1 env antibody A32 | protein | 218 | 8% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.70 | 0.75 | 98 | CL |
| 2 | 692 | 0.67 | 0.75 | 53 | empty |
| 3 | 647 | 0.64 | 0.75 | 51 | empty |
| 4 | 99 | 0.48 | 0.81 | 17 | empty |
| 5 | 143 | 0.43 | 0.75 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2018 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1887 Ų buried · 12 hydrogen bonds · protein-protein
- L–B · 288 Ų buried · 4 hydrogen bonds · protein-protein
- H–B · 260 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3TNM · Crystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody · 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 3TNM · PDBe 3TNM
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