MolNFT v1 · #72779 · protein

The structure of ubr box (rlges)

3NIN · E3 ubiquitin-protein ligase UBR1: “The structure of ubr box (rlges)”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.54). MolNFT v1 #72779 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NIN
Type: protein
Length: 167 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase UBR1; Peptide rlges
UniProt: P19812
Ligands: ZN
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E3 ubiquitin-protein ligase UBR1	protein	80	11% helix, 21% strand	P19812
D	Peptide rlges	protein	4	0% helix, 50% strand	—
E	Peptide rlges	protein	3	0% helix, 33% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.54	0.77	27	empty

Interfaces

3 interfaces between chains.

A–B · 442 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 411 Å² buried · 13 hydrogen bonds · protein-protein
B–E · 343 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3NIN · The structure of UBR box (RLGES) · the same entry in another collection · chain A against A, 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 0.96

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 3NIN · PDBe 3NIN · UniProt P19812

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