› 6xer

X-ray diffraction
2.5Å resolution

Tubulin-RB3_SLD in complex with colchicine

Released:
DOI: 10.2210/pdb6xer/pdb
Model geometry
Fit model/data
PDB entry 6xer coloured by chain, front view.
PDB entry 6xer coloured by chain, side view.
PDB entry 6xer coloured by chain, top view.
Source organisms:
Primary publication:
Design, Synthesis, and Biological Evaluation of Stable Colchicine-Binding Site Tubulin Inhibitors 6-Aryl-2-benzoyl-pyridines as Potential Anticancer Agents.
Chen H, Deng S, Albadari N, Yun MK, Zhang S, Li Y, Ma D, Parke DN, Yang L, Seagroves TN, White SW, Miller DD, Li W
J Med Chem 64 12049-12074 (2021)
PMID: 34378386

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-135916 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Tubulin alpha-1B chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 438 amino acids
Theoretical weight: 48.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2XVP4 (Residues: 1-438; Coverage: 97%)
Gene name: TUBA1B
Sequence domains:
Tubulin beta chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 433 amino acids
Theoretical weight: 48.65 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P02554 (Residues: 1-433; Coverage: 97%)
Sequence domains:
Stathmin-4 Chain: E

Ligands and Environments

5 bound ligands:
Ligand GTP 3 x GTP
Ligand MG 2 x MG
Ligand SO4 3 x SO4
Ligand GDP 1 x GDP
Ligand LOC 2 x LOC
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 65.717Å b: 127.025Å c: 254.208Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.223
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Recent Advances of Tubulin Inhibitors Targeting the Colchicine Binding Site for Cancer Therapy.
Hawash M. (2022)
1 more

2 mentions without citation

Design, Synthesis, and Biological Evaluation of Stable Colchicine-Binding Site Tubulin Inhibitors 6-Aryl-2-benzoyl-pyridines as Potential Anticancer Agents.
Chen et al. (2021)
1 more