Research workbench
Structure of 3E9 antibody Fab bound to marinobufagenin
Analyse Structure of 3E9 antibody Fab bound to marinobufagenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PYD
- Type
- protein
- Length
- 838 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IGG4 C region; 3E9…
- Ligands
- P4S
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IGG4 C region | protein | 210 | 6% helix, 53% strand | — |
| L | 3E9 antibody Fab light chain | protein | 208 | 6% helix, 51% strand | — |
| A | 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IGG4 C region | protein | 209 | 6% helix, 55% strand | — |
| B | 3E9 antibody Fab light chain | protein | 211 | 6% helix, 50% 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, A, B
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 | 892 | 0.70 | 0.75 | 83 | empty |
| 2 | 207 | 0.62 | 0.82 | 25 | P4S |
| 3 | 146 | 0.59 | 0.83 | 21 | P4S |
| 4 | 232 | 0.55 | 0.78 | 47 | empty |
| 5 | 225 | 0.53 | 0.77 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1802 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1797 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 184 Ų buried · 1 hydrogen bond · protein-protein
- H–B · 159 Ų buried · 0 hydrogen bonds · protein-protein
- L–A · 147 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6PYD · Structure of 3E9 antibody Fab bound to marinobufagenin · 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 6PYD · PDBe 6PYD
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