MolNFT v1 · #52047 · protein

Decoding of methylated histone H3 tail by the pygo-BCL9 wnt signaling complex

2VPD · Pygopus homolog 1: “Decoding of methylated histone H3 tail by the pygo-BCL9 wnt signaling complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.66). MolNFT v1 #52047 on GenesisL1: 3D structure, binding sites and…

PDB: 2VPD
Type: protein
Length: 194 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pygopus homolog 1; B-cell CLL/LYMPHOMA 9 protein
UniProt: Q9Y3Y4, O00512
Ligands: ZN
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pygopus homolog 1	protein	59	31% helix, 19% strand	Q9Y3Y4
B	B-cell CLL/LYMPHOMA 9 protein	protein	34	35% helix, 24% strand	O00512
C	Pygopus homolog 1	protein	66	26% helix, 23% strand	Q9Y3Y4
D	B-cell CLL/LYMPHOMA 9 protein	protein	35	34% helix, 26% strand	O00512

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, C

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

Pockets

2 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	513	0.66	0.77	44	empty
2	53	0.29	0.75	13	empty

Interfaces

6 interfaces between chains.

C–D · 692 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 676 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 539 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 532 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 117 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2VPD · Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y3Y4 · AlphaFold monomer V2.0 prediction for pygopus homolog 1 (Q9Y3Y4) · a predicted model of the same protein · chain A against A, TM-score 0.95
O00512 · AlphaFold monomer V2.0 prediction for B-cell CLL/LYMPHOMA 9 protein (O00512) · a predicted model of the same protein · chain B against A, TM-score 0.74

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 Q9Y3Y4
Every structure of UniProt O00512
Elsewhere: RCSB PDB 2VPD · PDBe 2VPD · UniProt Q9Y3Y4 · UniProt O00512

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