3IGU

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

Structural Biology Knowledgebase: 3IGU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IGU

Classification: HYDROLASE

Total Structure Weight: 96207.32

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-N-acetylgalactosaminidase A, B 400 Homo sapiens EC#: 3.2.1.49 IUBMB
Mutation: N201Q
Gene Name(s): NAGA Gene View

Small Molecules
Ligands 6 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)
7JZ
Query on 7JZ

A, B 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose
2-DEOXY-2,2-DIFLUORO-BETA-D-GALACTOPYRANOSYL- ENZYME INTERMEDIATE (Synonym)
C6 H10 F2 O5
SHBCJQOMZTUYEL-MGCNEYSASA-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)
FUC
Query on FUC

B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.164
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 151.61 α = 90.00
b = 113.65 β = 96.14
c = 68.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-28
  • Released Date: 2009-10-20
  • Deposition author(s): Clark, N.E., Garman, S.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor