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
- 1MCR
- 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-L-his-D-pro-oh
- Ligands
- ACE
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin lambda dimer mcg (light chain) | protein | 216 | 5% helix, 47% strand | — |
| P | Peptide N-acetyl-L-his-D-pro-oh | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B, P
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 | 708 | 0.67 | 0.76 | 64 | empty |
| 2 | 240 | 0.55 | 0.77 | 43 | ACE |
| 3 | 91 | 0.46 | 0.81 | 23 | empty |
| 4 | 50 | 0.25 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1865 Ų buried · 16 hydrogen bonds · protein-protein
- B–P · 194 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 141 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
- 1MCR · 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 1MCR · PDBe 1MCR
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