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The structure of ubr box (rdaa)

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

PDB: 3NIL
Type: protein
Length: 328 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase UBR1; Peptide rdaa
UniProt: P19812
Ligands: ZN
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F	E3 ubiquitin-protein ligase UBR1	protein	81	11% helix, 22% strand	P19812
B	E3 ubiquitin-protein ligase UBR1	protein	82	13% helix, 22% strand	P19812
X	Peptide rdaa	protein	3	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, D, F
ACT · Acetate ion · additive · 2 copies · chains B, F

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

Pockets

7 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	1104	0.83	0.84	100	ACT
2	58	0.49	0.86	17	empty
3	68	0.46	0.83	20	empty
4	71	0.37	0.78	18	empty
5	72	0.32	0.75	18	empty

Interfaces

8 interfaces between chains.

A–D · 540 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 435 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 375 Å² buried · 9 hydrogen bonds · protein-protein
D–X · 323 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 240 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3NIL · The structure of UBR box (RDAA) · 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 3NIL · PDBe 3NIL · UniProt P19812

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