MolNFT v1 · #160922 · protein
Structure of kappa-on-heavy (koh) antibody Fab bound to the cardiac hormone marinobufagenin
6PYC · Koh body Fab heavy chain: “Structure of kappa-on-heavy (koh) antibody Fab bound to the cardiac hormone marinobufagenin”. X-ray diffraction, 2 ligands (P4S, SO4), 8 pockets (best druggability 0.68). MolNFT v1 #160922 on GenesisL1: 3D…
- PDB
- 6PYC
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Koh body Fab heavy chain; Koh body Fab light chain; Anti-kappa antibody Fab heavy chain…
- Ligands
- P4S, SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Koh body Fab heavy chain | protein | 204 | 5% helix, 49% strand | — |
| L | Koh body Fab light chain | protein | 213 | 7% helix, 51% strand | — |
| A | Anti-kappa antibody Fab heavy chain | protein | 213 | 4% helix, 50% strand | — |
| B | Anti-kappa antibody Fab light chain | protein | 213 | 6% helix, 54% strand | — |
Ligands and binding sites
- P4S · (3beta,5beta,14alpha,15beta)-3,5-dihydroxy-14,15-epoxybufa-20,22-dienolide · ligand · 2 copies · chains H, L
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.68 | 0.75 | 70 | empty |
| 2 | 178 | 0.62 | 0.83 | 19 | P4S |
| 3 | 432 | 0.57 | 0.74 | 44 | empty |
| 4 | 212 | 0.52 | 0.77 | 33 | empty |
| 5 | 67 | 0.51 | 0.86 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1819 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1626 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 522 Ų buried · 7 hydrogen bonds · protein-protein
- L–B · 432 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6PYC · Structure of kappa-on-heavy (KoH) antibody Fab bound to the cardiac hormone… · 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
- Elsewhere: RCSB PDB 6PYC · PDBe 6PYC
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