3W3D | pdb_00003w3d

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 (Depositor), 0.192 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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
Modeled Residue Count: 634
Deposited Residue Count: 634
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(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

Help

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 (Depositor), 0.192 (DCC)

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

View Full Validation Report

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
Version 2.1: 2025-03-26
Changes: Data collection, Database references, Structure summary