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
- 1MCI
- Type
- protein
- Length
- 435 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-phe-L-his-D-pro-oh
- Ligands
- ACE
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin lambda dimer mcg (light chain) | protein | 216 | 5% helix, 45% strand | — |
| P | Peptide N-acetyl-D-phe-L-his-D-pro-oh | protein | 3 | 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 | 864 | 0.71 | 0.76 | 71 | empty |
| 2 | 216 | 0.59 | 0.80 | 35 | empty |
| 3 | 103 | 0.42 | 0.77 | 25 | empty |
| 4 | 68 | 0.32 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1828 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 221 Ų buried · 2 hydrogen bonds · protein-protein
- B–P · 214 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 d-amino, 1 covalent (disulfide, D-amino acid, covalent ligand).
Compared structures
- 1MCI · 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 1MCI · PDBe 1MCI
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