MolNFT v1 · #31683 · protein

Tandem chromodomains of human CHD1

2B2Y · Chromodomain-helicase-DNA-binding protein 1: “Tandem chromodomains of human CHD1”. X-ray diffraction, 7 pockets (best druggability 0.85). MolNFT v1 #31683 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2B2Y
Type: protein
Length: 430 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromodomain-helicase-DNA-binding protein 1
UniProt: O14646
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromodomain-helicase-DNA-binding protein 1	protein	175	42% helix, 25% strand	O14646
B	Chromodomain-helicase-DNA-binding protein 1	protein	169	45% helix, 21% strand	O14646
C	Chromodomain-helicase-DNA-binding protein 1	protein	86	31% helix, 28% strand	O14646

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	936	0.85	0.86	113	empty
2	99	0.46	0.80	20	empty
3	100	0.45	0.79	23	empty
4	137	0.45	0.76	18	empty
5	50	0.44	0.83	9	empty

Interfaces

3 interfaces between chains.

A–B · 1375 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 310 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 303 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2B2Y · Tandem chromodomains of human CHD1 · the same entry in another collection · chain A against A, TM-score 1.00
O14646 · AlphaFold monomer V2.0 prediction for chromodomain-helicase-DNA- binding protein 1… · 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 O14646
Elsewhere: RCSB PDB 2B2Y · PDBe 2B2Y · UniProt O14646

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