Research workbench

DAB3/HOIP-rbr apo structure

Analyse DAB3/HOIP-rbr apo structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SC6
Type: protein
Length: 604 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase RNF31; Single domain antibody
EC: 2.3.2.31
UniProt: Q96EP0
Ligands: ZN, SO4, CL
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31)	protein	365	36% helix, 12% strand	Q96EP0
B	Single domain antibody	protein	119	5% helix, 50% strand	—
C	Single domain antibody	protein	120	8% helix, 50% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

7 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	74	0.75	0.98	29	empty
2	977	0.72	0.76	85	SO4
3	250	0.49	0.74	30	empty
4	173	0.44	0.75	28	SO4
5	156	0.43	0.75	28	SO4

Interfaces

3 interfaces between chains.

A–C · 959 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 951 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 721 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6SC6 · dAb3/HOIP-RBR apo structure · the same entry in another collection · chain A against A, TM-score 1.00
Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain A against A, TM-score 0.59

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 Q96EP0
Elsewhere: RCSB PDB 6SC6 · PDBe 6SC6 · UniProt Q96EP0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.