2ORJ

crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with N-acetyl mannosamine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pulmonary surfactant-associated protein D
A, B, C
160Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35247
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BM3
Query on BM3
Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]		2-acetamido-2-deoxy-alpha-D-mannopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-UOLFYFMNSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.63α = 90
b = 108.33β = 91.51
c = 55.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2007-05-08 
    • Deposition Author(s): Head, J.F.

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary