6Z2S | pdb_00006z2s

Crystal structure of adhibin analogue-bound myosin-2

PDB DOI: https://doi.org/10.2210/pdb6Z2S/pdb

Classification: MOTOR PROTEIN
Organism(s): Dictyostelium discoideum
Expression System: Dictyostelium discoideum
Mutation(s): No

Deposited: 2020-05-18 Released: 2021-06-09
Deposition Author(s): Ewert, W., Knoelker, H.-J., Tsiavaliaris, G., Preller, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

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

The synthetic carbazole adhibin acts as selective myosin class-IX inhibitor in lung cancer cells

Bader, A., Ewert, W., Knoelker, H.-J., Preller, M., Tsiavaliaris, G.

To be published.

Macromolecule Content

Total Structure Weight: 91.56 kDa
Atom Count: 5,885
Modeled Residue Count: 748
Deposited Residue Count: 788
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin-2 heavy chain	A	788	Dictyostelium discoideum	Mutation(s): 0 Gene Names: mhcA, DDB_G0286355
UniProt
Find proteins for P08799 (Dictyostelium discoideum) Explore P08799 Go to UniProtKB: P08799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08799
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AD9 Query on AD9 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]	ADP METAVANADATE C₁₀ H₁₆ N₅ O₁₃ P₂ V XLVFTLJPBLXCED-KWIZKVQNSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Q5Q (Subject of Investigation/LOI) Query on Q5Q Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3,6-dibromo-1-(hydroxymethyl)carbazole C₁₃ H₉ Br₂ N O LFOHIKGNXVHWSB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], H [auth A], I [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.931	α = 90
b = 144.22	β = 90
c = 156.937	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	PR 1478/2-1

Revision History (Full details and data files)

Version 1.0: 2021-06-09
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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Crystal structure of adhibin analogue-bound myosin-2

The synthetic carbazole adhibin acts as selective myosin class-IX inhibitor in lung cancer cells

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations