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Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

Analyse Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RSD
Type: protein
Length: 68 residues
Chains: 1
Method: solution nmr
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: NOT
Source: Oryza sativa Japonica Group
Molecule: E3 SUMO-protein ligase SIZ1
EC: 6.3.2.-
UniProt: Q6L4L4
Ligands: ZN
Pockets: 1 · best druggability 0.31

Structure

solution nmr · resolution NOT · 1 distinct chain · 10% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 SUMO-protein ligase SIZ1 (EC 6.3.2.-)	protein	68	10% helix, 13% strand	Q6L4L4

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.31	0.75	15	empty

Compared structures

2RSD · Solution structure of the plant homeodomain (phd) of the E3 sumo ligase SIZ1 from rice · the same entry in another collection · chain A against A, TM-score 1.00
Q6L4L4 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase SIZ1 (Q6L4L4) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 Q6L4L4
Elsewhere: RCSB PDB 2RSD · PDBe 2RSD · UniProt Q6L4L4

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