MolNFT v1 · #73980 · protein

Crystal structure of the A20 ZNF4 and ubiquitin complex

3OJ3: “Crystal structure of the A20 ZNF4 and ubiquitin complex”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.70). MolNFT v1 #73980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OJ3
Type: protein
Length: 828 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; Tumor necrosis factor alpha-induced protein 3
UniProt: P0CG47, P21580
Ligands: ZN
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F	Ubiquitin	protein	73	21% helix, 36% strand	P0CG47
B	Ubiquitin	protein	72	21% helix, 36% strand	P0CG47
G, H	Ubiquitin	protein	71	21% helix, 34% strand	P0CG47
I	Tumor necrosis factor alpha-induced protein 3	protein	33	39% helix, 12% strand	P21580
J, N	Tumor necrosis factor alpha-induced protein 3	protein	30	40% helix, 13% strand	P21580
K, L, M, P	Tumor necrosis factor alpha-induced protein 3	protein	31	39% helix, 13% strand	P21580
O	Tumor necrosis factor alpha-induced protein 3	protein	32	41% helix, 6% strand	P21580

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains I, J, K, L, M, N, O, P

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	619	0.70	0.78	60	empty
2	211	0.62	0.82	32	empty
3	338	0.57	0.76	37	empty
4	276	0.57	0.77	42	empty
5	256	0.57	0.78	35	empty

Interfaces

26 interfaces between chains.

A–I · 422 Å² buried · 5 hydrogen bonds · protein-protein
C–I · 412 Å² buried · 5 hydrogen bonds · protein-protein
G–O · 408 Å² buried · 4 hydrogen bonds · protein-protein
F–N · 396 Å² buried · 6 hydrogen bonds · protein-protein
B–K · 391 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3OJ3 · Crystal structure of the A20 ZnF4 and ubiquitin complex · the same entry in another collection · chain P against P, TM-score 1.00

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 P0CG47
Every structure of UniProt P21580
Elsewhere: RCSB PDB 3OJ3 · PDBe 3OJ3 · UniProt P0CG47 · UniProt P21580

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