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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.286 (Depositor), 0.290 (DCC)
R-Value Work:
0.222 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Discovery and Design of novel Tubulin inhibitors

Zhang, H., Luo, C.

To be published.

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

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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	440	Bos taurus	Mutation(s): 0 EC: 3.6.5
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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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	378	Gallus gallus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 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 U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain U [auth C] mmCIF format, chain G [auth A] mmCIF format, chain U [auth C]	G [auth A], U [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain U [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain HA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain HA [auth F]	HA [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain HA [auth F] Interactions & Density Focus chain HA [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain M [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain M [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain M [auth B]	DA [auth D], M [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain DA [auth D] Focus chain M [auth B] Interactions & Density Focus chain DA [auth D] Focus chain M [auth B]
97O Query on 97O Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	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		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	FA [auth D] GA [auth D] I [auth A] J [auth A] L [auth A] 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		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C]	AA [auth C], BA [auth C], CA [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Z [auth C] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth C]	K [auth A], P [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain K [auth A] Focus chain P [auth B] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	EA [auth D], H [auth A], N [auth B], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain H [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain EA [auth D] Focus chain H [auth A] Focus chain N [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.286 (Depositor), 0.290 (DCC)
R-Value Work: 0.222 (Depositor), 0.220 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Zhang, H.

Luo, C.

Revision History (Full details and data files)

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