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Crystal structure of ZYG11B bound to ggfn degron

Analyse Crystal structure of ZYG11B bound to ggfn degron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EP2
Type: protein
Length: 1,137 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein zyg-11 homolog B
UniProt: Q9C0D3
Pockets: 11 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein zyg-11 homolog B	protein	286	74% helix, 1% strand	Q9C0D3
D	Protein zyg-11 homolog B	protein	284	74% helix, 1% strand	Q9C0D3
B	Protein zyg-11 homolog B	protein	281	72% helix, 1% strand	Q9C0D3

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.70	0.78	64	empty
2	266	0.69	0.84	26	empty
3	315	0.67	0.82	31	empty
4	131	0.56	0.82	18	empty
5	229	0.55	0.77	26	empty

Interfaces

5 interfaces between chains.

A–B · 1016 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 978 Å² buried · 21 hydrogen bonds · protein-protein
C–B · 750 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 746 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 109 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7EP2 · Crystal structure of ZYG11B bound to GGFN degron · the same entry in another collection · chain A against A, TM-score 1.00
Q9C0D3 · AlphaFold monomer V2.0 prediction for protein zyg-11 homolog B (Q9C0D3) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q9C0D3
Elsewhere: RCSB PDB 7EP2 · PDBe 7EP2 · UniProt Q9C0D3

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