MolNFT v1 · #165806 · protein

Crystal structure of S. cerevisiae sumo E3 ligase SIZ2

6U75 · E3 sumo-protein ligase SIZ2: “Crystal structure of S. cerevisiae sumo E3 ligase SIZ2”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.49). MolNFT v1 #165806 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6U75
Type: protein
Length: 522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 sumo-protein ligase SIZ2
EC: 2.3.2.-
UniProt: Q12216
Ligands: ZN
Pockets: 6 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 sumo-protein ligase SIZ2 (EC 2.3.2.-)	protein	261	20% helix, 30% strand	Q12216
B	E3 sumo-protein ligase SIZ2 (EC 2.3.2.-)	protein	261	21% helix, 30% strand	Q12216

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.49	0.77	33	empty
2	99	0.40	0.76	18	empty
3	93	0.37	0.75	15	empty
4	51	0.35	0.79	13	empty
5	62	0.27	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 241 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6U75 · Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ2 · the same entry in another collection · chain A against A, TM-score 1.00
Q12216 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase SIZ2 (Q12216) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q12216
Elsewhere: RCSB PDB 6U75 · PDBe 6U75 · UniProt Q12216

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