MolNFT v1 · #161737 · protein

Clathrin heavy chain N-terminal domain bound to GTSE1 lidl motif

6QNP · Clathrin heavy chain 1: “Clathrin heavy chain N-terminal domain bound to GTSE1 lidl motif”. X-ray diffraction, 15 pockets (best druggability 0.83). MolNFT v1 #161737 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QNP
Type: protein
Length: 1,519 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clathrin heavy chain 1; G2 and S phase-expressed protein 1
UniProt: Q00610, Q9NYZ3
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Clathrin heavy chain 1	protein	361	7% helix, 50% strand	Q00610
B	Clathrin heavy chain 1	protein	360	7% helix, 50% strand	Q00610
C	Clathrin heavy chain 1	protein	356	8% helix, 50% strand	Q00610
D	Clathrin heavy chain 1	protein	354	7% helix, 49% strand	Q00610
H, I	G2 and S phase-expressed protein 1	protein	20	0% helix, 10% strand	Q9NYZ3
J	G2 and S phase-expressed protein 1	protein	24	0% helix, 8% strand	Q9NYZ3
K	G2 and S phase-expressed protein 1	protein	24	0% helix, 8% strand	Q9NYZ3

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1105	0.83	0.84	131	empty
2	571	0.72	0.80	63	empty
3	610	0.71	0.79	73	empty
4	606	0.71	0.79	67	empty
5	443	0.68	0.80	39	empty

Interfaces

12 interfaces between chains.

C–J · 1302 Å² buried · 13 hydrogen bonds · protein-protein
D–K · 1302 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 1198 Å² buried · 12 hydrogen bonds · protein-protein
B–I · 1198 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 819 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6QNP · Clathrin heavy chain N-terminal domain bound to GTSE1 lidl motif · the same entry in another collection · chain K against K, TM-score 1.00
Q00610 · AlphaFold monomer V2.0 prediction for clathrin heavy chain 1 (Q00610) · 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 Q00610
Every structure of UniProt Q9NYZ3
Elsewhere: RCSB PDB 6QNP · PDBe 6QNP · UniProt Q00610 · UniProt Q9NYZ3

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