Research workbench
IGG1 Fab fragment (83.1) complex with 16-residue peptide (residues 304-321 of HIV-1 GP120 (mn isolate))
Analyse IGG1 Fab fragment (83.1) complex with 16-residue peptide (residues 304-321 of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NAK
- Type
- protein
- Length
- 882 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 83.1 - light chain; Fab 83.1 - heavy chain; Peptide MP1
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Fab 83.1 - light chain | protein | 217 | 6% helix, 51% strand | — |
| H, I | Fab 83.1 - heavy chain | protein | 214 | 6% helix, 53% strand | — |
| P, Q | Peptide MP1 | protein | 10 | 0% helix, 0% strand | — |
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 | 697 | 0.73 | 0.79 | 54 | empty |
| 2 | 720 | 0.73 | 0.79 | 94 | empty |
| 3 | 192 | 0.59 | 0.82 | 38 | empty |
| 4 | 324 | 0.58 | 0.77 | 47 | empty |
| 5 | 174 | 0.53 | 0.79 | 31 | empty |
Interfaces
9 interfaces between chains.
- M–I · 1715 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 1680 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 821 Ų buried · 2 hydrogen bonds · protein-protein
- I–Q · 360 Ų buried · 7 hydrogen bonds · protein-protein
- H–P · 327 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NAK · IGG1 Fab fragment (83.1) complex with 16-residue peptide (residues 304-321 of HIV-1 GP120… · 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 1NAK · PDBe 1NAK
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