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Crystal structure of STUB1 with a macrocyclic peptide

Analyse Crystal structure of STUB1 with a macrocyclic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TB1
Type: protein
Length: 273 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase chip; Ala-cys-ser-ser-ile-TRP-cys-pro-asp-gly
EC: 2.3.2.27
UniProt: Q9UNE7
Ligands: I1J
Pockets: 1 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase chip (EC 2.3.2.27)	protein	127	80% helix, 0% strand	Q9UNE7
B	E3 ubiquitin-protein ligase chip (EC 2.3.2.27)	protein	126	79% helix, 0% strand	Q9UNE7
C, D	Ala-cys-ser-ser-ile-TRP-cys-pro-asp-gly	protein	10	0% helix, 0% strand	—

Ligands and binding sites

I1J · 1,3-bis(sulfanyl)propan-2-one · ligand · 2 copies · chains B, C, A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	975	0.79	0.81	75	I1J

Interfaces

5 interfaces between chains.

A–B · 689 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 581 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 571 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 85 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 80 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7TB1 · Crystal structure of STUB1 with a macrocyclic peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q9UNE7 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase chip (Q9UNE7) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9UNE7
Elsewhere: RCSB PDB 7TB1 · PDBe 7TB1 · UniProt Q9UNE7

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