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: 1MCF
Type: protein
Length: 438 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin lambda-1 light chain; Peptide N-acetyl-L-gln-D-phe-L-his-D-pro-B-ala-B-ala…
UniProt: P0DOX8
Ligands: ACE
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Immunoglobulin lambda-1 light chain	protein	216	6% helix, 50% strand	P0DOX8
P	Peptide N-acetyl-L-gln-D-phe-L-his-D-pro-B-ala-B-ala-oh	protein	6	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

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.68	0.96	21	empty
2	678	0.66	0.75	57	empty
3	217	0.63	0.83	34	empty
4	144	0.44	0.76	24	empty
5	68	0.35	0.77	22	empty

Interfaces

3 interfaces between chains.

A–B · 1853 Å² buried · 24 hydrogen bonds · protein-protein
A–P · 369 Å² buried · 5 hydrogen bonds · protein-protein
B–P · 281 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 2 d-amino, 2 modified, 1 covalent (disulfide, D-amino acid, nonstandard, covalent ligand).

Compared structures

1MCF · 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 1MCF · PDBe 1MCF · UniProt P0DOX8

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