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Crystal structure of A20, 2.5 ångström

Analyse Crystal structure of A20, 2.5 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DKB
Type: protein
Length: 2,112 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor, alpha-induced protein 3
EC: 3.-.-.-
UniProt: P21580
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Tumor necrosis factor, alpha-induced protein 3 (EC 3.-.-.-)	protein	352	37% helix, 16% strand	P21580

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1112	0.80	0.81	105	empty
2	877	0.79	0.82	81	empty
3	990	0.78	0.80	75	empty
4	769	0.77	0.81	53	empty
5	612	0.70	0.79	86	empty

Interfaces

5 interfaces between chains.

D–F · 1006 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 970 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 909 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 864 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 851 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3DKB · Crystal Structure of A20, 2.5 angstrom · the same entry in another collection · chain C against C, TM-score 1.00
P21580 · AlphaFold monomer V2.0 prediction for tumor necrosis factor alpha- induced protein 3… · a predicted model of the same protein · chain A 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 P21580
Elsewhere: RCSB PDB 3DKB · PDBe 3DKB · UniProt P21580

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