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Structure of an endocytic receptor

Analyse Structure of an endocytic receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JPU
Type: protein
Length: 4,623 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lymphocyte antigen 75
UniProt: O60449
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 14% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Lymphocyte antigen 75	protein	1156	14% helix, 22% strand	O60449
D	Lymphocyte antigen 75	protein	1155	14% helix, 22% strand	O60449

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.87	0.88	147	empty
2	1016	0.86	0.87	139	empty
3	1108	0.85	0.86	142	empty
4	918	0.82	0.84	102	empty
5	970	0.78	0.80	124	empty

Interfaces

4 interfaces between chains.

C–D · 2652 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2592 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 1440 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1391 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 80 disulfide (disulfide).

Compared structures

7JPU · Structure of an endocytic receptor · the same entry in another collection · chain A against A, TM-score 1.00
O60449 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 75 (O60449) · a predicted model of the same protein · chain D against A, TM-score 0.41

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 O60449
Elsewhere: RCSB PDB 7JPU · PDBe 7JPU · UniProt O60449

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