MolNFT v1 · #187120 · protein

Crystal structure of alpha-cop-WD40 domain

7S22 · Coatomer subunit alpha: “Crystal structure of alpha-cop-WD40 domain”. X-ray diffraction, 1 ligand (ACE), 7 pockets (best druggability 0.83). MolNFT v1 #187120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7S22
Type: protein
Length: 924 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coatomer subunit alpha
UniProt: Q96WV5
Ligands: ACE
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coatomer subunit alpha	protein	307	2% helix, 56% strand	Q96WV5
B	Coatomer subunit alpha	protein	313	3% helix, 55% strand	Q96WV5
C	Coatomer subunit alpha	protein	304	2% helix, 56% strand	Q96WV5

Ligands and binding sites

ACE · Acetyl group · ligand · 3 copies · chains A, B, C

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

Pockets

7 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	777	0.83	0.85	52	empty
2	775	0.83	0.85	53	empty
3	786	0.82	0.85	52	empty
4	712	0.65	0.74	89	empty
5	248	0.51	0.75	36	empty

Interfaces

3 interfaces between chains.

A–B · 540 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 533 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 283 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

7S22 · Crystal structure of alpha-COP-WD40 domain · the same entry in another collection · chain A against A, TM-score 1.00
Q96WV5 · AlphaFold monomer V2.0 prediction for putative coatomer subunit alpha (Q96WV5) · a predicted model of the same protein · chain C 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 Q96WV5
Elsewhere: RCSB PDB 7S22 · PDBe 7S22 · UniProt Q96WV5

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