Research workbench

Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin- box motif

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

PDB: 5M5S
Type: protein
Length: 754 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clathrin heavy chain 1; Amphiphysin
UniProt: P49951, P49418
Pockets: 6 · best druggability 0.82

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	Amphiphysin	protein	7	0% helix, 14% strand	P49418
G, H	Amphiphysin	protein	10	0% helix, 0% strand	P49418

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

6 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	1128	0.82	0.83	123	GOL
2	676	0.74	0.80	73	GOL
3	53	0.35	0.78	14	empty
4	67	0.31	0.75	16	empty
5	51	0.28	0.75	17	empty

Interfaces

6 interfaces between chains.

A–B · 1082 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 538 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 534 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 507 Å² buried · 6 hydrogen bonds · protein-protein
B–H · 503 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5M5S · Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif · 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 B against A, TM-score 0.99
P49418 · AlphaFold monomer V2.0 prediction for amphiphysin (P49418) · a predicted model of the same protein · chain E against A, TM-score 0.53

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 P49418
Elsewhere: RCSB PDB 5M5S · PDBe 5M5S · UniProt P49951 · UniProt P49418

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