Research workbench
Structure antibody F9 in complex with methylated peptide
Analyse Structure antibody F9 in complex with methylated peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDV
- Type
- protein
- Length
- 424 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Oryctolagus cuniculus; SYNTHETIC CONSTRUCT
- Molecule
- Fab heavy chain; Fab light chain; Gly-M3L-gly-gly-thr-tyr-pro
- Ligands
- IOD
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.9 · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 203 | 6% helix, 53% strand | — |
| L | Fab light chain | protein | 214 | 7% helix, 53% strand | — |
| P | Gly-M3L-gly-gly-thr-tyr-pro | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 8 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.62 | 0.74 | 57 | empty |
| 2 | 61 | 0.46 | 0.84 | 22 | IOD |
| 3 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1766 Ų buried · 14 hydrogen bonds · protein-protein
- H–P · 535 Ų buried · 11 hydrogen bonds · protein-protein
- L–P · 211 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, methylation).
Compared structures
- 6LDV · Structure antibody F9 in complex with methylated peptide · 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 6LDV · PDBe 6LDV
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