MolNFT v1 · #37273 · protein

Catalytic domain of cdy

2FW2 · Testis-specific chromodomain protein Y 2: “Catalytic domain of cdy”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #37273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2FW2
Type: protein
Length: 1,545 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Testis-specific chromodomain protein Y 2
UniProt: Q9Y6F7
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 55% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Testis-specific chromodomain protein Y 2	protein	258	54% helix, 16% strand	Q9Y6F7
B	Testis-specific chromodomain protein Y 2	protein	255	55% helix, 16% strand	Q9Y6F7
C	Testis-specific chromodomain protein Y 2	protein	256	55% helix, 16% strand	Q9Y6F7
D	Testis-specific chromodomain protein Y 2	protein	257	54% helix, 16% strand	Q9Y6F7
E	Testis-specific chromodomain protein Y 2	protein	259	55% helix, 16% strand	Q9Y6F7
F	Testis-specific chromodomain protein Y 2	protein	260	55% helix, 15% strand	Q9Y6F7

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	416	0.86	0.93	74	empty
2	698	0.84	0.88	110	empty
3	165	0.70	0.89	27	empty
4	150	0.64	0.86	27	empty
5	257	0.58	0.79	41	empty

Interfaces

10 interfaces between chains.

E–F · 1256 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1247 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 1242 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1240 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 1223 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2FW2 · Catalytic domain of CDY · the same entry in another collection · chain C against C, TM-score 1.00
Q9Y6F7 · AlphaFold monomer V2.0 prediction for testis-specific chromodomain protein Y 2 (Q9Y6F7) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 Q9Y6F7
Elsewhere: RCSB PDB 2FW2 · PDBe 2FW2 · UniProt Q9Y6F7

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