7VMJ

Crystal structure of tubulin with 17a

PDB DOI: https://doi.org/10.2210/pdb7VMJ/pdb

Classification: STRUCTURAL PROTEIN/INHIBITOR
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-08 Released: 2022-10-19
Deposition Author(s): Jifa, Z., Lun, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.243
R-Value Work: 0.199
R-Value Observed: 0.200

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of tubulin with 17j

Jifa, Z., Lun, T.

To be published.

Macromolecule Content

Total Structure Weight: 264.21 kDa
Atom Count: 17,608
Modelled Residue Count: 2,190
Deposited Residue Count: 2,317
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	450	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	445	Bos taurus	Mutation(s): 0 Gene Names: TUBB2B
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	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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(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C]	G [auth A], P [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain P [auth C]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D]	K [auth B], S [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain S [auth D]
7PU (Subject of Investigation/LOI) Query on 7PU Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	N-[3-[[6-[[3-[bis(fluoranyl)methyl]phenyl]amino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide C₂₁ H₁₉ F₂ N₅ O JQXVFDHRPZGRPG-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	M [auth B], N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [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 R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain R [auth C]	I [auth A], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain R [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C]	H [auth A], L [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C]