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Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1)

Analyse Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M5U
Type: protein
Length: 746 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clathrin heavy chain 1; Large delta antigen
UniProt: P49951, P0C6L6
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Clathrin heavy chain 1	protein	360	8% helix, 52% strand	P49951
E, F	Large delta antigen	protein	7	0% helix, 14% strand	P0C6L6
G, H	Large delta antigen	protein	6	0% helix, 0% strand	P0C6L6

Ligands and binding sites

GOL · Glycerol · additive · chains A

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	688	0.78	0.83	83	empty
2	603	0.74	0.81	69	empty
3	427	0.72	0.82	54	empty
4	63	0.31	0.75	17	empty
5	59	0.29	0.75	17	empty

Interfaces

6 interfaces between chains.

A–B · 939 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 474 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 452 Å² buried · 5 hydrogen bonds · protein-protein
A–G · 323 Å² buried · 3 hydrogen bonds · protein-protein
B–H · 321 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5M5U · Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D… · the same entry in another collection · chain H against H, TM-score 1.00
P49951 · AlphaFold monomer V2.0 prediction for clathrin heavy chain 1 (P49951) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P49951
Every structure of UniProt P0C6L6
Elsewhere: RCSB PDB 5M5U · PDBe 5M5U · UniProt P49951 · UniProt P0C6L6

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