5Z4P | pdb_00005z4p

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

• PDB DOI: https://doi.org/10.2210/pdb5Z4P/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
• Mutation(s): No 


• Deposited: 2018-01-12 Released: 2019-01-16 
• Deposition Author(s): Zhang, H., Luo, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Discovery and Design of novel Tubulin inhibitors

Zhang, H., Luo, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 264.38 kDa 
• Atom Count: 17,477 
• Modeled Residue Count: 2,161 
• Deposited Residue Count: 2,305 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	440	Bos taurus	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947  Go to UniProtKB:  P81947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	431	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856  Go to UniProtKB:  Q6B856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	185	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043  Go to UniProtKB:  P63043

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	378	Gallus gallus	Mutation(s): 0

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	G [auth A], U [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	HA [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	DA [auth D], M [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
97O	R [auth B]	6,7,8-trimethoxy-1-(4-methoxyphenyl)-4,5-dihydro-2~{H}-benzo[e]indazole C21 H22 N2 O4 LOJZGYGSTOWCFA-UHFFFAOYSA-N
MES	Q [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	FA [auth D], GA [auth D], I [auth A], J [auth A], L [auth A], O [auth B], S [auth C], T [auth C], W [auth C], X [auth C], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	AA [auth C], BA [auth C], CA [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	K [auth A], P [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	EA [auth D], H [auth A], N [auth B], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.832	α = 90
b = 154.843	β = 90
c = 181.024	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Zhang, H., Luo, C.

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 2.0: 2019-08-28
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description