Research workbench
Crystal structure of 10E8V4 Fab in complex with an HIV-1 GP41 peptide.
Analyse Crystal structure of 10E8V4 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
- 5IQ9
- Type
- protein
- Length
- 910 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10E8V4 heavy chain; 10E8V4 light chain; GP41 mper peptide
- UniProt
- P01857, P0CG05, Q1HSF8
- Pockets
- 13 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | 10E8V4 heavy chain | protein | 227 | 7% helix, 53% strand | P01857 |
| B, L | 10E8V4 light chain | protein | 210 | 9% helix, 50% strand | P0CG05 |
| C, P | GP41 mper peptide | protein | 18 | 67% helix, 0% strand | Q1HSF8 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.62 | 0.77 | 62 | empty |
| 2 | 565 | 0.61 | 0.74 | 65 | empty |
| 3 | 67 | 0.55 | 0.88 | 19 | empty |
| 4 | 335 | 0.53 | 0.74 | 42 | empty |
| 5 | 244 | 0.52 | 0.76 | 33 | empty |
Interfaces
9 interfaces between chains.
- H–L · 2214 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2198 Ų buried · 22 hydrogen bonds · protein-protein
- H–P · 711 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 693 Ų buried · 5 hydrogen bonds · protein-protein
- B–L · 423 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5IQ9 · Crystal structure of 10E8v4 Fab in complex with an HIV-1 gp41 peptide. · the same entry in another collection · chain A against A, 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 Q1HSF8
- Elsewhere: RCSB PDB 5IQ9 · PDBe 5IQ9 · UniProt P01857 · UniProt P0CG05 · UniProt Q1HSF8
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