7VMK

Crystal structure of tubulin with 3

PDB DOI: https://doi.org/10.2210/pdb7VMK/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: 2.50 Å
R-Value Free: 0.232
R-Value Work: 0.194
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of tubulin with 3

Jifa, Z., Lun, T.

To be published.

Macromolecule Content

Total Structure Weight: 264.91 kDa
Atom Count: 17,937
Modelled Residue Count: 2,199
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
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 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 S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain S [auth C]	G [auth A], S [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain S [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain W [auth F] MOL2 format, chain W [auth F]	W [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain W [auth F] Interactions & Density Focus chain W [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain V [auth D] MOL2 format, chain K [auth B] MOL2 format, chain V [auth D]	K [auth B], V [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain V [auth D] Interactions & Density Focus chain K [auth B] Focus chain V [auth D]
7PL (Subject of Investigation/LOI) Query on 7PL Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	N-[3-[[6-[[3-(trifluoromethyl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide C₂₁ H₁₈ F₃ N₅ O YOHYSYJDKVYCJI-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 N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	N [auth B], O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B]	Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C]	I [auth A], J [auth A], M [auth B], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain U [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C]	H [auth A], L [auth B], P [auth B], T [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth B] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth B] Focus chain T [auth C]