1PWB

High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose

PDB DOI: https://doi.org/10.2210/pdb1PWB/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-07-01 Released: 2003-08-05
Deposition Author(s): Shrive, A.K., Tharia, H.A., Strong, P., Kishore, U., Burns, I., Rizkallah, P.J., Reid, K.B., Greenhough, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.228
R-Value Work: 0.205
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 57.57 kDa
Atom Count: 4,038
Modelled Residue Count: 452
Deposited Residue Count: 531
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 D	A, B, C	177	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P35247 (Homo sapiens) Explore P35247 Go to UniProtKB: P35247
PHAROS: P35247 GTEx: ENSG00000133661
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35247
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	2		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C]	H [auth B], L [auth C]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth B] Focus chain L [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	D	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.228
R-Value Work: 0.205
R-Value Observed: 0.205
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.48	α = 90
b = 108.3	β = 91.43
c = 55.78	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-08-05
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-27
Changes: Database references, Structure summary
Version 2.2: 2023-08-16
Changes: Data collection, Refinement description

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Help and Resources

1PWB

High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2