2VYP | pdb_00002vyp

Rabbit-muscle G-actin in complex with myxobacterial rhizopodin

PDB DOI: https://doi.org/10.2210/pdb2VYP/pdb

Classification: CONTRACTILE PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2008-07-25 Released: 2009-02-24
Deposition Author(s): Hagelueken, G., Albrecht, S.C., Steinmetz, H., Jansen, R., Heinz, D.W., Kalesse, M., Schubert, W.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.241 (Depositor), 0.306 (DCC)
R-Value Work:
0.186 (Depositor), 0.273 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The Absolute Configuration of Rhizopodin and its Inhibition of Actin Polymerization by Dimerization.

Hagelueken, G., Albrecht, S.C., Steinmetz, H., Jansen, R., Heinz, D.W., Kalesse, M., Schubert, W.-D.

(2009) Angew Chem Int Ed Engl 48: 595

PubMed: 19035596 Search on PubMed
DOI: https://doi.org/10.1002/anie.200802915
Primary Citation Related Structures:
2VYP

Organizational Affiliation

Research Group Molecular Host-Pathogen Interactions, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.

Macromolecule Content

Total Structure Weight: 87.19 kDa
Atom Count: 5,844
Modeled Residue Count: 688
Deposited Residue Count: 754
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIN, ALPHA SKELETAL MUSCLE	A, B	377	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RH9 Query on RH9 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	RHIZOPODIN C₇₈ H₁₂₄ N₄ O₂₂ MWDPPGCTEBRUNT-IKBNIWNCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B]	D [auth A], I [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.241 (Depositor), 0.306 (DCC)
R-Value Work: 0.186 (Depositor), 0.273 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.653	α = 90
b = 194.863	β = 90
c = 53.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-24
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

2VYP | pdb_00002vyp

Rabbit-muscle G-actin in complex with myxobacterial rhizopodin

Literature

The Absolute Configuration of Rhizopodin and its Inhibition of Actin Polymerization by Dimerization.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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