MolNFT v1 · #72784 · protein

The structure of ubr box (NATIVE2)

3NIS · E3 ubiquitin-protein ligase UBR1: “The structure of ubr box (NATIVE2)”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.84). MolNFT v1 #72784 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NIS
Type: protein
Length: 327 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase UBR1
UniProt: P19812
Ligands: ZN
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	E3 ubiquitin-protein ligase UBR1	protein	82	12% helix, 22% strand	P19812
D	E3 ubiquitin-protein ligase UBR1	protein	81	12% helix, 19% strand	P19812

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, D, F
ACT · Acetate ion · additive · 3 copies · chains A, B, D, F

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.84	0.85	95	ACT
2	102	0.51	0.82	26	empty

Interfaces

6 interfaces between chains.

A–F · 497 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 489 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 436 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 261 Å² buried · 2 hydrogen bonds · protein-protein
D–F · 183 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3NIS · The structure of UBR box (native2) · the same entry in another collection · chain B against B, TM-score 1.00
P19812 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UBR1 (P19812) · a predicted model of the same protein · chain A 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 P19812
Elsewhere: RCSB PDB 3NIS · PDBe 3NIS · UniProt P19812

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