4AVV

Structure of CPHPC bound to Serum Amyloid P Component


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.150

Literature

Macromolecules
Sequence Display for 4AVV

Classification: SUGAR BINDING PROTEIN

Total Structure Weight: 126340.34

Macromolecule Entities
Molecule Chains Length Organism Details
SERUM AMYLOID P-COMPONENT A, B, C, D, E 204 Homo sapiens Gene Name(s): APCS Gene View PTX2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GHE
Query on GHE

A, B, C, D, E (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]- 6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid
C16 H24 N2 O6
HZLAWYIBLZNRFZ-VXGBXAGGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIA
Query on SIA

B, D O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D, E N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

D BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

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

A, B, C, D, E CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B, E ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GHE N/A in BindingDB
Kd: 8.8 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.150
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 154.38 α = 90.00
b = 108.58 β = 138.53
c = 120.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-29
  • Released Date: 2013-06-19
  • Deposition author(s): Kolstoe, S.E., Jenvey, M.C., Wood, S.P.

Revision History

  • 2014-08-06
    Type: Database references
  • 2014-10-22
    Type: Database references