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Structure of the ESCRT-I endosomal trafficking complex

Analyse Structure of the ESCRT-I endosomal trafficking complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F66
Type: protein
Length: 480 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Saccharomyces cerevisiae
Molecule: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine…
UniProt: P25604, Q02767, Q99176
Ligands: SO4
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · resolution 2.8 · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease	protein	65	82% helix, 0% strand	P25604
B, E	Vacuolar protein sorting-associated protein VPS28	protein	111	63% helix, 0% strand	Q02767
C	Protein SRN2	protein	65	80% helix, 0% strand	Q99176
F	Protein SRN2	protein	63	78% helix, 0% strand	Q99176

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, D, F, C, E

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

Pockets

8 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	515	0.78	0.85	78	SO4
2	144	0.74	0.92	27	empty
3	182	0.72	0.89	35	empty
4	99	0.48	0.81	28	empty
5	117	0.45	0.78	18	empty

Interfaces

9 interfaces between chains.

A–B · 1381 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1343 Å² buried · 18 hydrogen bonds · protein-protein
B–E · 963 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 876 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 866 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2F66 · Structure of the escrt-I endosomal trafficking complex · the same entry in another collection · chain F against F, TM-score 1.00
P25604 · AlphaFold monomer V2.0 prediction for suppressor protein STP22 of temperature-sensitive… · a predicted model of the same protein · chain A against A, TM-score 0.95
Q99176 · AlphaFold monomer V2.0 prediction for protein SRN2 (Q99176) · a predicted model of the same protein · chain F against A, TM-score 0.93
Q02767 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 28… · a predicted model of the same protein · chain B against A, TM-score 0.77

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 P25604
Every structure of UniProt Q02767
Every structure of UniProt Q99176
Elsewhere: RCSB PDB 2F66 · PDBe 2F66 · UniProt P25604 · UniProt Q02767 · UniProt Q99176

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