MolNFT v1 · #72778 · protein

The structure of ubr box (rraa)

3NIM · E3 ubiquitin-protein ligase UBR1: “The structure of ubr box (rraa)”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.84). MolNFT v1 #72778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NIM
Type: protein
Length: 329 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase UBR1; Peptide rraa
UniProt: P19812
Ligands: ZN
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E3 ubiquitin-protein ligase UBR1	protein	82	12% helix, 22% strand	P19812
D	E3 ubiquitin-protein ligase UBR1	protein	80	13% helix, 19% strand	P19812
F	E3 ubiquitin-protein ligase UBR1	protein	81	11% helix, 20% strand	P19812
X	Peptide rraa	protein	4	0% helix, 25% 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

4 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	1150	0.84	0.85	96	empty
2	106	0.47	0.80	25	empty
3	64	0.29	0.74	16	empty
4	60	0.28	0.74	15	empty

Interfaces

8 interfaces between chains.

A–F · 445 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 439 Å² buried · 12 hydrogen bonds · protein-protein
F–X · 415 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 392 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 309 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3NIM · The structure of UBR box (RRAA) · 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 0.96

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 3NIM · PDBe 3NIM · UniProt P19812

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