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Crystal structure of the chs-B30.2 domains of TRIM20

Analyse Crystal structure of the chs-B30.2 domains of TRIM20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CG4
Type: protein
Length: 2,240 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrin
UniProt: O15553
Ligands: DHL, ACE, SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Pyrin	protein	376	45% helix, 20% strand	O15553
B	Pyrin	protein	363	46% helix, 21% strand	O15553
E	Pyrin	protein	373	46% helix, 20% strand	O15553

Ligands and binding sites

DHL · 2-amino-ethanethiol · ligand · 5 copies · chains C, D, E, F
ACE · Acetyl group · ligand · 4 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 8 copies · chains B, C, D, E, F
EDO · 1,2-ethanediol · additive · 2 copies · chains B, D

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.76	0.79	68	empty
2	683	0.76	0.81	81	empty
3	124	0.68	0.89	22	empty
4	647	0.67	0.76	51	SO4
5	411	0.64	0.78	48	empty

Interfaces

9 interfaces between chains.

E–F · 5241 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 5090 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 4905 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 1453 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1220 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 covalent (covalent ligand).

Compared structures

4CG4 · Crystal structure of the CHS-B30.2 domains of TRIM20 · the same entry in another collection · chain F against F, TM-score 1.00
O15553 · AlphaFold monomer V2.0 prediction for pyrin (O15553) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 O15553
Elsewhere: RCSB PDB 4CG4 · PDBe 4CG4 · UniProt O15553

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