MolNFT v1 · #137565 · protein
CH1/CKAPPA Fab mutant 15.1
5VSI · CH1/CKAPPA Fab heavy chain: “CH1/CKAPPA Fab mutant 15.1”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.66). MolNFT v1 #137565 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VSI
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH1/CKAPPA Fab heavy chain; CH1/CKAPPA Fab light chain
- UniProt
- Q6GMX6, Q7Z3Y4
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CH1/CKAPPA Fab heavy chain | protein | 221 | 10% helix, 52% strand | Q6GMX6 |
| L | CH1/CKAPPA Fab light chain | protein | 212 | 6% helix, 54% strand | Q7Z3Y4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains H, L
- EDO · 1,2-ethanediol · additive · 4 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.66 | 0.75 | 70 | empty |
| 2 | 60 | 0.63 | 0.93 | 18 | EDO |
| 3 | 64 | 0.36 | 0.77 | 13 | EDO |
| 4 | 68 | 0.30 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- H–L · 1851 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5VSI · CH1/Ckappa Fab mutant 15.1 · the same entry in another collection · chain H against H, 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 Q6GMX6
- Every structure of UniProt Q7Z3Y4
- Elsewhere: RCSB PDB 5VSI · PDBe 5VSI · UniProt Q6GMX6 · UniProt Q7Z3Y4
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