MolNFT v1 · #100381 · protein

Crystal structure of sumo E3 ligase PIAS3

4MVT · E3 sumo-protein ligase PIAS3: “Crystal structure of sumo E3 ligase PIAS3”. X-ray diffraction, 3 ligands (ZN, UNX, CL), 9 pockets (best druggability 0.60). MolNFT v1 #100381 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4MVT
Type: protein
Length: 1,008 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 sumo-protein ligase PIAS3
EC: 6.3.2.-
UniProt: Q9Y6X2
Ligands: ZN, UNX, CL
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 sumo-protein ligase PIAS3 (EC 6.3.2.-)	protein	255	21% helix, 33% strand	Q9Y6X2
B	E3 sumo-protein ligase PIAS3 (EC 6.3.2.-)	protein	251	22% helix, 32% strand	Q9Y6X2
C	E3 sumo-protein ligase PIAS3 (EC 6.3.2.-)	protein	253	21% helix, 32% strand	Q9Y6X2
D	E3 sumo-protein ligase PIAS3 (EC 6.3.2.-)	protein	249	22% helix, 32% strand	Q9Y6X2

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
UNX · Unknown atom or ion · ion · 32 copies · chains A, D, B, C
CL · Chloride ion · ion · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	307	0.60	0.78	46	CL, UNX
2	338	0.59	0.77	38	UNX
3	255	0.57	0.78	30	UNX
4	257	0.56	0.77	35	UNX
5	255	0.56	0.77	30	UNX

Interfaces

3 interfaces between chains.

A–D · 463 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 459 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 451 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4MVT · Crystal structure of SUMO E3 Ligase PIAS3 · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y6X2 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase PIAS3 (Q9Y6X2) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 Q9Y6X2
Elsewhere: RCSB PDB 4MVT · PDBe 4MVT · UniProt Q9Y6X2

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