5ZXH | pdb_00005zxh

The structure of MT189-tubulin complex

PDB DOI: https://doi.org/10.2210/pdb5ZXH/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Sus scrofa, Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-05-21 Released: 2019-05-22
Deposition Author(s): Li, Z.P., Wang, Y.X., Meng, T., Yang, J.L., Chen, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.259 (Depositor), 0.254 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The Structure of MT189-Tubulin Complex Provides Insights into Drug Design

Li, Z.P., Ma, L.L., Wu, C.Y., Meng, T., Ma, L.P., Zheng, W., Yu, Y., Chen, Q., Yang, J.L., Shen, J.G.

(2019) Lett Drug Des Discov

DOI: https://doi.org/10.2174/1570180816666181122122655

Macromolecule Content

Total Structure Weight: 265.07 kDa
Atom Count: 17,367
Modeled Residue Count: 2,151
Deposited Residue Count: 2,317
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	450	Sus scrofa	Mutation(s): 0 Gene Names: TUBA1B EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 2 Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL

Small Molecules

Ligands 7 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 P [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	G [auth A], P [auth C], S [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth C] Focus chain S [auth D]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F] mmCIF format, chain V [auth F]	V [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
9LX (Subject of Investigation/LOI) Query on 9LX Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain O [auth B] mmCIF format, chain U [auth D] mmCIF format, chain O [auth B]	O [auth B], U [auth D]	2-(6-fluoro-3-{[(4-methoxyphenyl)methyl]amino}imidazo[1,2-a]pyridin-2-yl)phenol C₂₁ H₁₈ F N₃ O₂ QBNMSKFVSPKNSV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain U [auth D] Interactions & Density Focus chain O [auth B] Focus chain U [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B]	L [auth B], N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain L [auth B] Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C]	I [auth A], M [auth B], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	H [auth A], K [auth B], Q [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D]