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The structure of ubr box (reaa)

Analyse The structure of ubr box (reaa) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NIK
Type: protein
Length: 330 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase UBR1; Peptide reaa
UniProt: P19812
Ligands: ZN
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	E3 ubiquitin-protein ligase UBR1	protein	82	12% helix, 22% strand	P19812
F	E3 ubiquitin-protein ligase UBR1	protein	80	13% helix, 19% strand	P19812
X	Peptide reaa	protein	4	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, D, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1126	0.84	0.85	93	empty
2	54	0.40	0.82	19	empty
3	57	0.30	0.75	15	empty
4	51	0.29	0.76	16	empty
5	63	0.28	0.73	17	empty

Interfaces

9 interfaces between chains.

A–B · 506 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 505 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 407 Å² buried · 12 hydrogen bonds · protein-protein
D–X · 321 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 319 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3NIK · The structure of UBR box (REAA) · the same entry in another collection · chain X against X, 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 F against A, TM-score 0.95

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 3NIK · PDBe 3NIK · UniProt P19812

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