Research workbench
APOBEC3B antibody 5G7 fv-clasp
Analyse APOBEC3B antibody 5G7 fv-clasp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KM6
- Type
- protein
- Length
- 672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5G7 human monoclonal Fab light chain; 5G7 human monoclonal Fab heavy chain
- Ligands
- NA, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 5G7 human monoclonal Fab light chain | protein | 165 | 28% helix, 35% strand | — |
| H | 5G7 human monoclonal Fab heavy chain | protein | 170 | 29% helix, 36% strand | — |
| l | 5G7 human monoclonal Fab light chain | protein | 166 | 28% helix, 34% strand | — |
| h | 5G7 human monoclonal Fab heavy chain | protein | 171 | 29% helix, 36% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains H, l
- CL · Chloride ion · ion · 3 copies · chains L, l
- EDO · 1,2-ethanediol · additive · 10 copies · chains L, H, h, l
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.79 | 0.83 | 78 | empty |
| 2 | 559 | 0.74 | 0.82 | 51 | empty |
| 3 | 316 | 0.68 | 0.82 | 44 | empty |
| 4 | 209 | 0.62 | 0.82 | 36 | empty |
| 5 | 209 | 0.62 | 0.82 | 33 | empty |
Interfaces
6 interfaces between chains.
- l–h · 2483 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 2450 Ų buried · 14 hydrogen bonds · protein-protein
- H–h · 703 Ų buried · 6 hydrogen bonds · protein-protein
- L–l · 375 Ų buried · 1 hydrogen bond · protein-protein
- L–h · 250 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7KM6 · APOBEC3B antibody 5G7 Fv-clasp · 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 7KM6 · PDBe 7KM6
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