Research workbench
Crystal structure of 10E8-S74W Fab in complex with an HIV-1 GP41 peptide.
Analyse Crystal structure of 10E8-S74W Fab in complex with an HIV-1 GP41 peptide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IQ7
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10E8-S74W heavy chain; 10E8-S74W light chain; GP41 mper peptide
- UniProt
- P01857, P0CG05, V9QIE5
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 10E8-S74W heavy chain | protein | 233 | 4% helix, 51% strand | P01857 |
| L | 10E8-S74W light chain | protein | 212 | 7% helix, 49% strand | P0CG05 |
| P | GP41 mper peptide | protein | 29 | 83% helix, 0% strand | V9QIE5 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.68 | 0.75 | 75 | empty |
| 2 | 203 | 0.55 | 0.79 | 35 | empty |
| 3 | 81 | 0.53 | 0.85 | 20 | empty |
| 4 | 112 | 0.44 | 0.78 | 26 | empty |
| 5 | 52 | 0.42 | 0.83 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2147 Ų buried · 18 hydrogen bonds · protein-protein
- H–P · 579 Ų buried · 4 hydrogen bonds · protein-protein
- L–P · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5IQ7 · Crystal structure of 10E8-S74W Fab in complex with an HIV-1 gp41 peptide. · 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 P01857
- Every structure of UniProt P0CG05
- Every structure of UniProt V9QIE5
- Elsewhere: RCSB PDB 5IQ7 · PDBe 5IQ7 · UniProt P01857 · UniProt P0CG05 · UniProt V9QIE5
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