› 5xag

X-ray diffraction
2.56Å resolution

Crystal structure of tubulin-stathmin-TTL-Compound Z2 complex

Released:
DOI: 10.2210/pdb5xag/pdb
PDB entry 5xag coloured by chain, front view.
PDB entry 5xag coloured by chain, side view.
PDB entry 5xag coloured by chain, top view.
Source organisms:
Primary publication:
Design, synthesis, biological evaluation and cocrystal structures with tubulin of chiral β-lactam bridged combretastatin A-4 analogues as potent antitumor agents.
Zhou P, Liang Y, Zhang H, Jiang H, Feng K, Xu P, Wang J, Wang X, Ding K, Luo C, Liu M, Wang Y
Eur J Med Chem 144 817-842 (2018)
PMID: 29306206

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-237153 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Tubulin alpha-1B chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 451 amino acids
Theoretical weight: 50.2 KDa
Source organism: Bos taurus
Expression system: Bos taurus
UniProt:
  • Canonical: P81947 (Residues: 1-451; Coverage: 100%)
Sequence domains:
Structure domains:
Tubulin beta-2B chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 445 amino acids
Theoretical weight: 50 KDa
Source organism: Bos taurus
Expression system: Bos taurus
UniProt:
  • Canonical: Q6B856 (Residues: 1-445; Coverage: 100%)
Gene name: TUBB2B
Sequence domains:
Structure domains:
Stathmin-4 Chain: E
Molecule details ›
Chain: E
Length: 189 amino acids
Theoretical weight: 22.13 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P63043 (Residues: 1-189; Coverage: 100%)
Gene name: Stmn4
Sequence domains: Stathmin family
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Tubulin tyrosine ligase Chain: F
Molecule details ›
Chain: F
Length: 378 amino acids
Theoretical weight: 43.55 KDa
Source organism: Gallus gallus
Expression system: Escherichia coli
Structure domains:

Ligands and Environments

9 bound ligands:
Ligand GTP 2 x GTP
Ligand MG 5 x MG
Ligand GOL 12 x GOL
Ligand CA 3 x CA
Ligand GDP 2 x GDP
Ligand MES 1 x MES
Ligand 93X 2 x 93X
Ligand IMD 3 x IMD
Ligand ACP 1 x ACP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 104.27Å b: 156.117Å c: 182.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.255
Expression systems:
  • Bos taurus
  • Escherichia coli

Quick links

Citations

2 review citations

Antitubulin sulfonamides: The successful combination of an established drug class and a multifaceted target.
Vicente-Blázquez et al. (2019)
1 more

1 mention without citation

Molecular interactions at the colchicine binding site in tubulin: An X-ray crystallography perspective.
Wang et al. (2022)