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Crystal structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila ciboulot and the C-terminal domain (residues 18-44) of bovine thymosin-BETA4, bound to G-actin-ATP

Analyse Crystal structure of a chimera containing the N-terminal domain (residues 8-29)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U8X
Type: protein
Length: 756 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Thymosin beta-4
UniProt: P68135, P62326, O97428
Ligands: ATP, MG
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Actin, alpha skeletal muscle	protein	357	45% helix, 20% strand	P68135
B, D	Thymosin beta-4	protein	21	57% helix, 5% strand	P62326, O97428

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 2 copies · chains A, C

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	331	0.75	0.86	52	ATP, MG
2	351	0.72	0.84	54	ATP, MG
3	572	0.64	0.75	50	empty
4	220	0.60	0.80	34	empty
5	221	0.58	0.79	34	empty

Interfaces

3 interfaces between chains.

A–B · 804 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 801 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 250 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3U8X · Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of… · the same entry in another collection · chain A against A, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain C against A, TM-score 0.98
P62326 · AlphaFold monomer V2.0 prediction for thymosin beta-4 (P62326) · a predicted model of the same protein · chain B against A, TM-score 0.40

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 P68135
Every structure of UniProt P62326
Every structure of UniProt O97428
Elsewhere: RCSB PDB 3U8X · PDBe 3U8X · UniProt P68135 · UniProt P62326 · UniProt O97428

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