Research workbench
Fab fragment (MN14C11.6) in complex with a peptide antigen derived from neisseria meningitidis P1.7 serosubtype antigen and domain II from streptococcal protein G
Analyse Fab fragment (MN14C11.6) in complex with a peptide antigen derived from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QKZ
- Type
- protein
- Length
- 501 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein G-prime; Antibody; Major outer membrane protein P1.16
- UniProt
- Q54181, Q06140
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein G-prime | protein | 58 | 24% helix, 47% strand | Q54181 |
| H | Antibody | protein | 219 | 5% helix, 47% strand | — |
| L | Antibody | protein | 214 | 6% helix, 52% strand | — |
| P | Major outer membrane protein P1.16 | protein | 10 | 0% helix, 20% strand | Q06140 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.56 | 0.75 | 45 | empty |
| 2 | 146 | 0.47 | 0.77 | 36 | empty |
| 3 | 166 | 0.45 | 0.75 | 24 | empty |
| 4 | 117 | 0.41 | 0.76 | 25 | empty |
| 5 | 58 | 0.31 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1874 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 565 Ų buried · 13 hydrogen bonds · protein-protein
- H–P · 493 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 169 Ų buried · 1 hydrogen bond · protein-protein
- A–L · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1QKZ · Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria… · 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 Q54181
- Every structure of UniProt Q06140
- Elsewhere: RCSB PDB 1QKZ · PDBe 1QKZ · UniProt Q54181 · UniProt Q06140
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