4WRE

Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D) Complexed with Inositol

PDB DOI: https://doi.org/10.2210/pdb4WRE/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Rattus norvegicus
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2014-10-23 Released: 2016-02-10
Deposition Author(s): Rynkiewicz, M.J., Wu, H., Cafarella, T.R., Nikolaidis, N.M., Head, J.F., Seaton, B.A., McCormack, F.X.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 ?
R-Value Free: 0.222
R-Value Work: 0.188
R-Value Observed: 0.191

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Differential ligand binding specificities of the pulmonary collectins are determined by the conformational freedom of a surface loop

Rynkiewicz, M.J., Wu, H., Cafarella, T.R., Nikolaidis, N.M., Head, J.F., Seaton, B.A., McCormack, F.X.

To be published.

Macromolecule Content

Total Structure Weight: 17.05 kDa
Atom Count: 1,204
Modelled Residue Count: 136
Deposited Residue Count: 148
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pulmonary surfactant-associated protein A	A	148	Rattus norvegicus	Mutation(s): 5 Gene Names: Sftpa1, Sftp-1, Sftp1, Sftpa
UniProt
Find proteins for P08427 (Rattus norvegicus) Explore P08427 Go to UniProtKB: P08427
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08427
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
INS Query on INS 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]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C₆ H₁₂ O₆ CDAISMWEOUEBRE-GPIVLXJGSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HEZ Query on HEZ 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]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 ?
R-Value Free: 0.222
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: H 3 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 66.73	α = 90
b = 66.73	β = 90
c = 165.891	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	#PO1-AI083222

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary

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Help and Resources

4WRE

Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D) Complexed with Inositol

Differential ligand binding specificities of the pulmonary collectins are determined by the conformational freedom of a surface loop

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)