MolNFT v1 · #14539 · protein
Principles and pitfalls in designing site directed peptide ligands
1MCJ · Immunoglobulin lambda dimer mcg (light chain): “Principles and pitfalls in designing site directed peptide ligands”. X-ray diffraction, 4 ligands (ACE, DPN, DPR), 2 pockets (best druggability 0.75). MolNFT v1 #14539 on GenesisL1: 3D…
- PDB
- 1MCJ
- Type
- protein
- Length
- 433 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-NH2
- Ligands
- ACE, DPN, DPR, NH2
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin lambda dimer mcg (light chain) | protein | 216 | 6% helix, 49% strand | — |
| P | Peptide N-acetyl-D-phe-L-his-D-pro-NH2 | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- DPN · D-phenylalanine · ligand · chains A, B, P
- DPR · D-proline · ligand · chains A, B, P
- NH2 · Amino group · ion · chains A, B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.75 | 0.78 | 123 | ACE, DPN, NH2 |
| 2 | 292 | 0.65 | 0.81 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1703 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 127 Ų buried · 1 hydrogen bond · protein-protein
- B–P · 83 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1MCJ · Principles and pitfalls in designing site directed peptide ligands · the same entry in another collection · chain P against P, 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 1MCJ · PDBe 1MCJ
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