3W3D

Crystal structure of smooth muscle G actin DNase I complex

PDB DOI: https://doi.org/10.2210/pdb3W3D/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Gallus gallus, Bos taurus
Mutation(s): No

Deposited: 2012-12-20 Released: 2013-01-30
Deposition Author(s): Sakabe, N., Sakabe, K., Sasaki, K., Kondo, H., Shimomur, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Work: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Refined structure and solvent network of chicken gizzard G-actin DNase 1 complex at 1.8A resolution

Sasaki, K., Sakabe, K., Sakabe, N., Kondo, H., Shimomur, M.

(1993) Acta Crystallogr A 49: C111-C112

Macromolecule Content

Total Structure Weight: 72.65 kDa
Atom Count: 5,472
Modelled Residue Count: 634
Deposited Residue Count: 634
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, gamma-enteric smooth muscle	A	374	Gallus gallus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P63270 (Gallus gallus) Explore P63270 Go to UniProtKB: P63270
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63270
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribonuclease-1	B	260	Bos taurus	Mutation(s): 0 EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus) Explore P00639 Go to UniProtKB: P00639
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00639
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G23450YU GlyCosmos: G23450YU GlyGen: G23450YU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Work: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42	α = 90
b = 225.3	β = 90
c = 77.4	γ = 90

Software Package:

Software Name	Purpose
WEIS	data scaling
BSS	data collection
X-PLOR	refinement
WEIS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary