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DAB3/HOIP-rbr-hoipin-8

Analyse DAB3/HOIP-rbr-hoipin-8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SC9
Type: protein
Length: 594 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: L68, ZN, SO4, CL
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31)	protein	355	35% helix, 11% strand	Q96EP0
B	Single domain antibody	protein	119	5% helix, 52% strand	—
C	Single domain antibody	protein	120	5% helix, 51% strand	—

Ligands and binding sites

L68 · 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-prop-1-enyl]-4-(1-methylpyrazol-4-yl) benzoic acid · ligand · chains A
ZN · Zinc ion · metal · 8 copies · chains A
SO4 · Sulfate ion · ion · 2 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

8 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	90	0.75	0.97	27	empty
2	1150	0.71	0.75	103	SO4, CL
3	56	0.52	0.87	16	empty
4	195	0.44	0.73	28	empty
5	159	0.43	0.75	29	SO4

Interfaces

3 interfaces between chains.

B–C · 956 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 929 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 718 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6SC9 · dAb3/HOIP-RBR-HOIPIN-8 · 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 0.60

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 6SC9 · PDBe 6SC9 · UniProt Q96EP0

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