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DAB3/HOIP-rbr-LIGAND3

Analyse DAB3/HOIP-rbr-LIGAND3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SC7
Type: protein
Length: 595 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: L6H, ZN, SO4, CL
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31)	protein	356	37% helix, 12% strand	Q96EP0
B	Single domain antibody	protein	119	5% helix, 51% strand	—
C	Single domain antibody	protein	120	5% helix, 52% strand	—

Ligands and binding sites

L6H · [2-[3-(cyclooct-4-en-1-yloxycarbonylamino)propylamino]-2-oxidanylidene-ethyl] (~{E})-4-[(2-oxidanylidene-5,6, 7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-2-enoate · ligand · chains A
ZN · Zinc ion · metal · 8 copies · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A, B
CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.74	0.97	22	empty
2	945	0.71	0.75	80	L6H, SO4
3	306	0.53	0.75	37	empty
4	176	0.46	0.75	28	empty
5	164	0.45	0.75	28	SO4

Interfaces

3 interfaces between chains.

A–C · 938 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 927 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 713 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

6SC7 · dAb3/HOIP-RBR-Ligand3 · the same entry in another collection · chain C against C, 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 0.60

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 6SC7 · PDBe 6SC7 · UniProt Q96EP0

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