MolNFT v1 · #102146 · protein
Crystal structure of human Fab CAP256-VRC26.07, a potent V1V2-directed HIV-1 neutralizing antibody
4OD3 · CAP256-VRC26.07 light chain: “Crystal structure of human Fab CAP256-VRC26.07, a potent V1V2-directed HIV-1 neutralizing antibody”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.69). MolNFT v1 #102146 on GenesisL1…
- PDB
- 4OD3
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP256-VRC26.07 light chain; CAP256-VRC26.07 heavy chain
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CAP256-VRC26.07 light chain | protein | 213 | 8% helix, 46% strand | — |
| H | CAP256-VRC26.07 heavy chain | protein | 234 | 6% helix, 50% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains L, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.69 | 0.76 | 78 | empty |
| 2 | 237 | 0.52 | 0.76 | 39 | empty |
| 3 | 63 | 0.35 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1821 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4OD3 · Crystal structure of human Fab CAP256-VRC26.07, a potent V1V2-directed HIV-1 neutralizing… · the same entry in another collection · chain L against L, 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 4OD3 · PDBe 4OD3
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