4KH2

Crystal structure of human alpha-L-iduronidase complex with 2-deoxy-2-fluoro-alpha-L-idopyranosyluronic acid fluoride

Structural Biology Knowledgebase: 4KH2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KH2

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 145153.55

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-L-iduronidase A, B 627 Homo sapiens EC#: 3.2.1.76 IUBMB
Fragment: UNP residues 27-653
Mutation: H33Q, Q63P, R105Q
Gene Name(s): IDUA Gene View

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

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

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

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

A, B 2-deoxy-2-fluoro-alpha-L-idopyranuronosyl fluoride, bound form
C6 H9 F O5
KRAJNEOUENOZDR-SKNVOMKLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SRT
Query on SRT

B S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TLA
Query on TLA

B L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.220
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 258.84 α = 90.00
b = 258.84 β = 90.00
c = 71.36 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-29
  • Released Date: 2013-09-18
  • Deposition author(s): Bie, H., Yin, J., He, X., Kermode, A.R., Goddard-Borger, E.D., Withers, S.G., James, M.N.G.

Revision History

  • 2013-11-06
    Type: Citation | Details: Citation update
  • 2013-09-25
    Type: Citation | Details: Citation update