1N7D

Extracellular domain of the LDL receptor

Structural Biology Knowledgebase: 1N7D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.382
  • R-Value Work: 0.381

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1N7D

Classification: LIPID TRANSPORT

Total Structure Weight: 88315.71

Macromolecule Entities
Molecule Chains Length Organism Details
Low-density lipoprotein receptor A 699 Homo sapiens Fragment: extracellular domain, RESIDUES 1-699
Mutation: N494Q, N636Q
Gene Name(s): LDLR Gene View

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KEG
Query on KEG

A 12-TUNGSTOPHOSPHATE
O40 P W12
WLQKSSFZMDTTCM-YEFKIAJVAA
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.382
  • R-Value Work: 0.381
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 185.29 α = 90.00
b = 185.29 β = 90.00
c = 85.19 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-11-13
  • Released Date: 2003-01-21
  • Deposition author(s): Rudenko, G., Henry, L., Henderson, K., Ichtchenko, K., Brown, M.S., Goldstein, J.L., Deisenhofer, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update