› 6d88

X-ray diffraction
2.85Å resolution

Tubulin-RB3_SLD-TTL in complex with compound 13f

Released:
DOI: 10.2210/pdb6d88/pdb
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PDB entry 6d88 coloured by chain, front view.
PDB entry 6d88 coloured by chain, side view.
PDB entry 6d88 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Modification of the 3,4,5-Trimethoxyphenyl Moiety in the Tubulin Inhibitor VERU-111 Leads to Improved Antiproliferative Activities.
Wang Q, Arnst KE, Wang Y, Kumar G, Ma D, Chen H, Wu Z, Yang J, White SW, Miller DD, Li W
J Med Chem 61 7877-7891 (2018)
PMID: 30122035

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-236967 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Tubulin alpha-1B chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 450 amino acids
Theoretical weight: 50.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2XVP4 (Residues: 1-450; Coverage: 100%)
Gene name: TUBA1B
Sequence domains:
Structure domains:
Tubulin beta chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 445 amino acids
Theoretical weight: 50 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P02554 (Residues: 1-445; Coverage: 100%)
Sequence domains:
Structure domains:
Stathmin-4 Chain: E
Tubulin tyrosine ligase Chain: F

Ligands and Environments

7 bound ligands:
Ligand GTP 2 x GTP
Ligand CA 2 x CA
Ligand MG 3 x MG
Ligand GDP 2 x GDP
Ligand MES 2 x MES
Ligand G9K 2 x G9K
Ligand ACP 1 x ACP
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 105.536Å b: 157.894Å c: 182.025Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.192 0.246
Expression system: Escherichia coli

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Citations

4 review citations

Colchicine-Binding Site Inhibitors from Chemistry to Clinic: A Review.
McLoughlin et al. (2020)
3 more

3 mentions without citation

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

PDB-REDO

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