4AMW

CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-idosyl- fluoride

Structural Biology Knowledgebase: 4AMW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 4AMW

Classification: LYASE

Total Structure Weight: 465671.06

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-1,4-GLUCAN LYASE ISOZYME 1 A, B, C, D 1027 Gracilariopsis lemaneiformis EC#: 4.2.2.13 IUBMB
Fragment: RESIDUES 62-1088
Gene Name(s): Ag111
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B9D
Query on B9D

A, B, C (2R,3R,4R,5S,6R)-6-fluoranyl-6-(hydroxymethyl)oxane- 2,3,4,5-tetrol
C6 H11 F O6
YQZCKDSOGGIGPL-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
5DI
Query on 5DI

D 2-OXO-1,2,DIDEOXY-5F-D-IDOPYRANOSE
C6 H9 F O5
VCJAHEOIRFFLTQ-SRQIZXRXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
5DI N/A in BindingDB
N/A in BindingMoad
Ki: 28300000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A, B, C, D L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.207
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.10 α = 80.31
b = 97.30 β = 83.29
c = 136.28 γ = 85.21

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-14
  • Released Date: 2013-03-27
  • Deposition author(s): Rozeboom, H.J., Yu, S., Madrid, S., Kalk, K.H., Dijkstra, B.W.

Revision History

  • 2013-09-25
    Type: Citation | Details: JRNL
  • 2013-08-14
    Type: Citation | Details: JRNL
  • 2013-08-14
    Type: Refinement description | Details: REMARK 3