MolNFT v1 · #119037 · protein

Yeast delta-cop-I mu-homology domain

5FK0 · Coatomer subunit delta: “Yeast delta-cop-I mu-homology domain”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.76). MolNFT v1 #119037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FK0
Type: protein
Length: 2,104 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coatomer subunit delta
UniProt: P43621
Ligands: CA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Coatomer subunit delta	protein	263	5% helix, 48% strand	P43621

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1200	0.76	0.78	101	empty
2	821	0.72	0.77	83	empty
3	1138	0.72	0.76	80	empty
4	777	0.71	0.77	78	empty
5	804	0.70	0.76	79	empty

Interfaces

15 interfaces between chains.

E–G · 724 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 663 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 644 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 642 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 629 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5FK0 · Yeast delta-COP-I mu-homology domain · the same entry in another collection · chain H against H, TM-score 1.00
P43621 · AlphaFold monomer V2.0 prediction for coatomer subunit delta (P43621) · a predicted model of the same protein · chain B 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 P43621
Elsewhere: RCSB PDB 5FK0 · PDBe 5FK0 · UniProt P43621

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