5LYJ

Tubulin-Combretastatin A4 complex

PDB DOI: https://doi.org/10.2210/pdb5LYJ/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-28 Released: 2017-01-18
Deposition Author(s): Gaspari, R., Prota, A.E., Cavalli, A., Steinmetz, M.O.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.217
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of cis- and trans-combretastatin binding to tubulin

Gaspari, R., Prota, A.E., Bargsten, K., Cavalli, A., Steinmetz, M.O.

(2017) Chem

DOI: https://doi.org/10.1016/j.chempr.2016.12.005

Macromolecule Content

Total Structure Weight: 265.29 kDa
Atom Count: 17,669
Modelled Residue Count: 2,186
Deposited Residue Count: 2,319
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-tyrosine ligase	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C]	G [auth A], Q [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain Q [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain X [auth F] MOL2 format, chain X [auth F]	X [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain X [auth F] Interactions & Density Focus chain X [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain K [auth B] MOL2 format, chain T [auth D] MOL2 format, chain K [auth B]	K [auth B], T [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain T [auth D] Interactions & Density Focus chain K [auth B] Focus chain T [auth D]
7BA Query on 7BA Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain M [auth B] MOL2 format, chain V [auth D] MOL2 format, chain M [auth B]	M [auth B], V [auth D]	Combretastatin A4 C₁₈ H₂₀ O₅ HVXBOLULGPECHP-WAYWQWQTSA-N		Interactions Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain W [auth E] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth E]	I [auth A], O [auth B], P [auth B], S [auth C], W [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth E] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain U [auth D] SDF format, chain H [auth A] SDF format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth C]	H [auth A], L [auth B], R [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain U [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
7BA	BindingDB: 5LYJ	Ki: 180 (nM) from 1 assay(s)
7BA	BindingDB: 5LYJ	IC50: min: 520, max: 4900 (nM) from 28 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.217
R-Value Work: 0.191
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.592	α = 90
b = 157.17	β = 90
c = 180.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_166608

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2017-05-17
Changes: Database references, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5LYJ

Tubulin-Combretastatin A4 complex

Structural basis of cis- and trans-combretastatin binding to tubulin

Entity ID: 1

UniProt

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Entity ID: 2

UniProt

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Entity ID: 3

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Entity ID: 4

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

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