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Crystal structure of a chimera containing the N-terminal domain (residues 8-24) of drosophila ciboulot and the C-terminal domain (residues 13-44) of bovine thymosin-BETA4, bound to G-actin-ATP

Analyse Crystal structure of a chimera containing the N-terminal domain (residues 8-24)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U9D
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, chimeric protein
UniProt: P68136, P62326, O97428
Ligands: ATP, MG
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Actin, alpha skeletal muscle	protein	357	41% helix, 21% strand	P68136
B, D	Thymosin beta-4, chimeric protein	protein	21	67% 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	373	0.75	0.86	50	ATP, MG
2	432	0.73	0.83	53	ATP, MG
3	589	0.65	0.76	52	empty
4	280	0.62	0.79	35	empty
5	241	0.58	0.78	35	empty

Interfaces

3 interfaces between chains.

A–B · 816 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 792 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 240 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3U9D · Crystal Structure of a chimera containing the N-terminal domain (residues 8-24) of… · the same entry in another collection · chain A against A, TM-score 1.00
P68136 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68136) · 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 0.37

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 P68136
Every structure of UniProt P62326
Every structure of UniProt O97428
Elsewhere: RCSB PDB 3U9D · PDBe 3U9D · UniProt P68136 · UniProt P62326 · UniProt O97428

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