Research workbench
Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 peptide mn
Analyse Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 peptide mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GO1
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 268-D, light chain; Fab 268-D, heavy chain; Envelope glycoprotein GP160
- UniProt
- P05877
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 268-D, light chain | protein | 209 | 8% helix, 49% strand | — |
| H | Fab 268-D, heavy chain | protein | 222 | 5% helix, 50% strand | — |
| P | Envelope glycoprotein GP160 | protein | 14 | 0% helix, 0% strand | P05877 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.64 | 0.75 | 67 | empty |
| 2 | 56 | 0.37 | 0.80 | 17 | empty |
| 3 | 52 | 0.27 | 0.74 | 20 | empty |
| 4 | 50 | 0.23 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1866 Ų buried · 28 hydrogen bonds · protein-protein
- L–P · 476 Ų buried · 6 hydrogen bonds · protein-protein
- H–P · 355 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3GO1 · Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 peptide MN · 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
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 3GO1 · PDBe 3GO1 · UniProt P05877
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