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
- 1MCE
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Immunoglobulin lambda-1 light chain; Peptide N-acetyl-L-gln-D-phe-L-his-D-pro-B-ala-oh
- UniProt
- P0DOX8
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin lambda-1 light chain | protein | 216 | 4% helix, 44% strand | P0DOX8 |
| P | Peptide N-acetyl-L-gln-D-phe-L-his-D-pro-B-ala-oh | protein | 5 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.66 | 0.88 | 26 | empty |
| 2 | 537 | 0.62 | 0.75 | 58 | empty |
| 3 | 175 | 0.59 | 0.82 | 32 | empty |
| 4 | 112 | 0.41 | 0.76 | 17 | empty |
| 5 | 102 | 0.36 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1785 Ų buried · 18 hydrogen bonds · protein-protein
- A–P · 318 Ų buried · 3 hydrogen bonds · protein-protein
- B–P · 234 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).
Compared structures
- 1MCE · Principles and pitfalls in designing site directed peptide ligands · the same entry in another collection · chain A against A, TM-score 1.00
- P0DOX8 · AlphaFold monomer V2.0 prediction for immunoglobulin lambda-1 light chain (P0DOX8) · a predicted model of the same protein · chain A against A, TM-score 0.51
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DOX8
- Elsewhere: RCSB PDB 1MCE · PDBe 1MCE · UniProt P0DOX8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.