3IKQ

Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D

Structural Biology Knowledgebase: 3IKQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IKQ

Classification: SUGAR BINDING PROTEIN

Total Structure Weight: 57446.63

Macromolecule Entities
Molecule Chains Length Organism Details
Pulmonary surfactant-associated protein D A, B, C 177 Homo sapiens Fragment: UNP residues 199-375
Mutation: P180S
Details: trimeric fragment comprising alpha helical neck and carbohydrate recognition domains
Gene Name(s): SFTPD Gene View COLEC7 PSPD SFTP4

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MAN
Query on MAN

A, B, C ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.202
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.91 α = 90.00
b = 108.78 β = 90.19
c = 56.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-06
  • Released Date: 2009-11-17
  • Deposition author(s): Shrive, A.K., Greenhough, T.J.

Revision History

  • 2014-02-19
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4