Research workbench
IGG1 Fab fragment (58.2) complex with 24-residue peptide (residues 308-333 of HIV-1 GP120 (mn isolate) with ala to aib substitution at position 323
Analyse IGG1 Fab fragment (58.2) complex with 24-residue peptide (residues 308-333 of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F58
- Type
- protein
- Length
- 455 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (IGG1 antibody 58.2 (light chain)); Protein (IGG1 antibody 58.2 (heavy chain))…
- UniProt
- P05877
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (IGG1 antibody 58.2 (light chain)) | protein | 216 | 5% helix, 54% strand | — |
| H | Protein (IGG1 antibody 58.2 (heavy chain)) | protein | 228 | 4% helix, 54% strand | — |
| P | Envelope glycoprotein GP120 | protein | 11 | 0% helix, 27% strand | P05877 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.45 | 0.77 | 23 | empty |
| 2 | 146 | 0.40 | 0.74 | 35 | empty |
| 3 | 53 | 0.27 | 0.74 | 19 | empty |
| 4 | 51 | 0.25 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1954 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 459 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 396 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1F58 · IGG1 Fab fragment (58.2) complex with 24-residue peptide (residues 308-333 of HIV-1 GP120… · 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
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 1F58 · PDBe 1F58 · UniProt P05877
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