Research workbench
Principles and pitfalls in designing site directed peptide ligands
Analyse Principles and pitfalls in designing site directed peptide ligands in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MCN
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin lambda dimer mcg (light chain); Peptide N-acetyl-D-his-L-pro-NH2
- Ligands
- ACE, NH2
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin lambda dimer mcg (light chain) | protein | 216 | 6% helix, 43% strand | — |
| P | Peptide N-acetyl-D-his-L-pro-NH2 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.67 | 0.75 | 66 | empty |
| 2 | 189 | 0.54 | 0.79 | 38 | empty |
| 3 | 56 | 0.54 | 0.88 | 20 | empty |
| 4 | 141 | 0.43 | 0.75 | 26 | empty |
| 5 | 85 | 0.40 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1738 Ų buried · 17 hydrogen bonds · protein-protein
- B–P · 174 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent, 1 d-amino (disulfide, covalent ligand, D-amino acid).
Compared structures
- 1MCN · Principles and pitfalls in designing site directed peptide ligands · the same entry in another collection · chain A against A, 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 1MCN · PDBe 1MCN
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