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The crystal structure of the N-terminal domain of COMMD9

Analyse The crystal structure of the N-terminal domain of COMMD9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OE9
Type: protein
Length: 235 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Comm domain-containing protein 9
UniProt: Q9P000
Ligands: K
Pockets: 3 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Comm domain-containing protein 9	protein	119	75% helix, 0% strand	Q9P000
B	Comm domain-containing protein 9	protein	116	77% helix, 0% strand	Q9P000

Ligands and binding sites

K · Potassium ion · metal · chains B
CIT · Citric acid · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	102	0.39	0.76	14	CIT
2	86	0.38	0.77	17	empty
3	51	0.30	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 669 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

4OE9 · The crystal structure of the n-terminal domain of COMMD9 · the same entry in another collection · chain A against A, TM-score 1.00
Q9P000 · AlphaFold monomer V2.0 prediction for comm domain-containing protein 9 (Q9P000) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9P000
Elsewhere: RCSB PDB 4OE9 · PDBe 4OE9 · UniProt Q9P000

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