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
- 1MCD
- Type
- protein
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin lambda-1 light chain; Peptide N-acetyl-D-phe-B-ala-L-his-D-pro-NH2
- UniProt
- P0DOX8
- Ligands
- ACE, NH2
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin lambda-1 light chain | protein | 216 | 6% helix, 54% strand | P0DOX8 |
| P | Peptide N-acetyl-D-phe-B-ala-L-his-D-pro-NH2 | protein | 4 | 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.69 | 0.76 | 74 | empty |
| 2 | 77 | 0.64 | 0.91 | 19 | empty |
| 3 | 76 | 0.41 | 0.79 | 24 | empty |
| 4 | 94 | 0.39 | 0.76 | 18 | empty |
| 5 | 55 | 0.32 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1901 Ų buried · 26 hydrogen bonds · protein-protein
- B–P · 246 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 183 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 d-amino, 1 covalent, 1 modified (disulfide, D-amino acid, covalent ligand, nonstandard).
Compared structures
- 1MCD · 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 1MCD · PDBe 1MCD · UniProt P0DOX8
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