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Complex between the leucine zipper (lz) and centrosomin-motif 2 (CM2) domains of drosophila melanogaster centrosomin (cnn) - L535E mutant form

Analyse Complex between the leucine zipper (lz) and centrosomin-motif 2 (CM2) domains… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MW9
Type: protein
Length: 450 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centrosomin
UniProt: P54623
Ligands: ZN
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 8 distinct chains · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Centrosomin	protein	66	92% helix, 0% strand	P54623
B	Centrosomin	protein	62	89% helix, 0% strand	P54623
C	Centrosomin	protein	46	89% helix, 0% strand	P54623
E	Centrosomin	protein	61	93% helix, 0% strand	P54623
F	Centrosomin	protein	64	91% helix, 0% strand	P54623
D	Centrosomin	protein	42	86% helix, 0% strand	P54623
H	Centrosomin	protein	57	88% helix, 0% strand	P54623
G	Centrosomin	protein	52	94% helix, 0% strand	P54623

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B, E, F

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

Pockets

4 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	167	0.53	0.79	16	empty
2	154	0.52	0.79	17	empty
3	90	0.37	0.75	13	empty
4	52	0.30	0.75	9	empty

Interfaces

12 interfaces between chains.

H–G · 1233 Å² buried · 1 hydrogen bond · protein-protein
A–B · 940 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 921 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 853 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 494 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5MW9 · Complex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (CM2) domains of… · the same entry in another collection · chain G against G, TM-score 1.00
P54623 · AlphaFold monomer V2.0 prediction for centrosomin (P54623) · a predicted model of the same protein · chain G against A, TM-score 0.95

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 P54623
Elsewhere: RCSB PDB 5MW9 · PDBe 5MW9 · UniProt P54623

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