6S8L | pdb_00006s8l

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes

PDB DOI: https://doi.org/10.2210/pdb6S8L/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2019-07-10 Released: 2019-11-27
Deposition Author(s): Sharma, A., Olieric, N., Steinmetz, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.266 (Depositor), 0.270 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes

La Sala, G., Olieric, N.

(2019) Chem

DOI: https://doi.org/10.1016/j.chempr.2019.08.022

Macromolecule Content

Total Structure Weight: 118.7 kDa
Atom Count: 8,691
Modeled Residue Count: 999
Deposited Residue Count: 1,058
Unique protein chains: 3

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	451	Homo sapiens	Mutation(s): 0 Gene Names: TUBA1B EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens) Explore P68363 Go to UniProtKB: P68363
PHAROS: P68363 GTEx: ENSG00000123416
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68363
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-3 chain	B	450	Homo sapiens	Mutation(s): 0 Gene Names: TUBB3, TUBB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13509 (Homo sapiens) Explore Q13509 Go to UniProtKB: Q13509
PHAROS: Q13509 GTEx: ENSG00000258947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13509
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed ankyrin repeat protein (DARPIN) D1	C [auth F]	157	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
PN6 (Subject of Investigation/LOI) Query on PN6 Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	(3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione C₁₉ H₂₀ N₄ O₂ UNRCMCRRFYFGFX-TYPNBTCFSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]