2VYP

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
R-Value Work: 0.186
R-Value Observed: 0.189

Starting Model: experimental
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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 of 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
Modelled Residue Count: 688
Deposited Residue Count: 754
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [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
R-Value Work: 0.186
R-Value Observed: 0.189
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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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

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Help and Resources

2VYP

Rabbit-muscle G-actin in complex with myxobacterial rhizopodin

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)