2DQY

Crystal structure of human carboxylesterase in complex with cholate and palmitate

Structural Biology Knowledgebase: 2DQY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.226

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DQY

Classification: HYDROLASE

Total Structure Weight: 183527.40

Macromolecule Entities
Molecule Chains Length Organism Details
Liver carboxylesterase 1 A, B, C 542 Homo sapiens EC#: 3.1.1.1 IUBMB
Fragment: residues 19-561
Mutation: ΔQ362
Gene Name(s): CES1 Gene View CES2 Gene View SES1

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

A, B, C CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIA
Query on SIA

A, B, C O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLM
Query on PLM

A, B, C PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.226
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 55.29 α = 90.00
b = 179.88 β = 90.00
c = 201.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-02
  • Released Date: 2006-08-29
  • Deposition author(s): Bencharit, S., Edwards, C.C., Morton, C.L., Howard-Williams, E.L., Potter, P.M., Redinbo, M.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values