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Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (AMPH4T1)

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

PDB: 5M5T
Type: protein
Length: 763 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clathrin heavy chain 1; Amphiphysin
UniProt: P49951, O08838
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 8% 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, J	Amphiphysin	protein	7	0% helix, 14% strand	O08838
G, H	Amphiphysin	protein	8	0% helix, 25% strand	O08838
I	Amphiphysin	protein	6	0% helix, 0% strand	O08838

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

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1073	0.83	0.84	120	empty
2	699	0.75	0.81	72	empty
3	126	0.41	0.75	25	empty
4	66	0.31	0.75	17	empty
5	55	0.31	0.76	16	empty

Interfaces

8 interfaces between chains.

A–B · 962 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 566 Å² buried · 7 hydrogen bonds · protein-protein
B–H · 563 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 524 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 522 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5M5T · Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide… · the same entry in another collection · chain J against J, 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
O08838 · AlphaFold monomer V2.0 prediction for amphiphysin (O08838) · a predicted model of the same protein · chain J against A, TM-score 0.57

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 O08838
Elsewhere: RCSB PDB 5M5T · PDBe 5M5T · UniProt P49951 · UniProt O08838

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