MolNFT v1 · #140210 · protein

Crystal structure of mouse CCD1 dix domain

5Y3B · Dixin: “Crystal structure of mouse CCD1 dix domain”. X-ray diffraction, 6 pockets (best druggability 0.81). MolNFT v1 #140210 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Y3B
Type: protein
Length: 575 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dixin
UniProt: Q80Y83
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, G	Dixin	protein	82	10% helix, 50% strand	Q80Y83
B, D	Dixin	protein	81	10% helix, 46% strand	Q80Y83
C	Dixin	protein	83	8% helix, 48% strand	Q80Y83
F	Dixin	protein	84	10% helix, 48% strand	Q80Y83

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	981	0.81	0.82	95	empty
2	1125	0.81	0.82	95	empty
3	385	0.66	0.80	42	empty
4	99	0.45	0.79	17	empty
5	102	0.38	0.75	22	empty

Interfaces

15 interfaces between chains.

C–D · 661 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 644 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 617 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 607 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 593 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5Y3B · Crystal structure of mouse Ccd1 DIX domain · the same entry in another collection · chain G against G, TM-score 1.00
Q80Y83 · AlphaFold monomer V2.0 prediction for dixin (Q80Y83) · a predicted model of the same protein · chain A 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 Q80Y83
Elsewhere: RCSB PDB 5Y3B · PDBe 5Y3B · UniProt Q80Y83

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