3G83
Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha 1,2 dimannose.
- PDB DOI: https://doi.org/10.2210/pdb3G83/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2009-02-11 Released: 2009-03-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.215 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Pulmonary surfactant-associated protein D | 160 | Homo sapiens | Mutation(s): 0  Gene Names: SFTPD, PSPD, SFTP4 | ||
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 AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900111 Query on PRD_900111 | D, E, F | 2alpha-alpha-mannobiose | Oligosaccharide / Metabolism |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.215 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 55.754 | α = 90 |
b = 108.774 | β = 91.58 |
c = 56.011 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
Entry History 
Deposition Data
- Released Date: 2009-03-17  Deposition Author(s): Head, J.F.
Revision History (Full details and data files)
- Version 1.0: 2009-03-17
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
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: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary