Research workbench
Crystal structure of human germline antibody IGHV1-69/IGKV3-20
Analyse Crystal structure of human germline antibody IGHV1-69/IGKV3-20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I17
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 213 | 5% helix, 50% strand | — |
| H | Fab heavy chain | protein | 213 | 4% helix, 50% strand | — |
| A | Fab light chain | protein | 214 | 7% helix, 47% strand | — |
| B | Fab heavy chain | protein | 216 | 8% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.77 | 0.81 | 85 | empty |
| 2 | 546 | 0.64 | 0.76 | 57 | empty |
| 3 | 389 | 0.61 | 0.77 | 51 | empty |
| 4 | 264 | 0.60 | 0.79 | 30 | empty |
| 5 | 270 | 0.57 | 0.78 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1803 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1717 Ų buried · 15 hydrogen bonds · protein-protein
- L–B · 454 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 178 Ų buried · 1 hydrogen bond · protein-protein
- H–B · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5I17 · Crystal structure of human germline antibody IGHV1-69/IGKV3-20 · 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 5I17 · PDBe 5I17
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