MolNFT v1 · #126543 · protein

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

5M61 · Clathrin heavy chain 1: “Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif”. X-ray diffraction, 7 pockets (best druggability 0.85). MolNFT v1 #126543 on GenesisL1: 3D structure, binding sites…

PDB: 5M61
Type: protein
Length: 762 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: 7 · best druggability 0.85

Structure

x-ray diffraction · 3 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	Amphiphysin	protein	9	0% helix, 11% strand	P49418
G, H	Amphiphysin	protein	12	0% helix, 0% strand	P49418

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	988	0.85	0.86	124	empty
2	645	0.74	0.81	68	empty
3	93	0.37	0.75	17	empty
4	57	0.30	0.75	16	empty
5	70	0.29	0.73	15	empty

Interfaces

6 interfaces between chains.

A–B · 1023 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 563 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 561 Å² buried · 7 hydrogen bonds · protein-protein
A–G · 533 Å² buried · 6 hydrogen bonds · protein-protein
B–H · 467 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5M61 · Clathrin heavy chain N-terminal domain bound to an extended 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 H against A, TM-score 0.33

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 5M61 · PDBe 5M61 · UniProt P49951 · UniProt P49418

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