1I7C

HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH METHYLGLYOXAL BIS-(GUANYLHYDRAZONE)

Structural Biology Knowledgebase: 1I7C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 1I7C

Classification: LYASE

Total Structure Weight: 38639.16

Macromolecule Entities
Molecule Chains Length Organism Details
S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN B 67 Homo sapiens EC#: 4.1.1.50 IUBMB
Gene Name(s): AMD1 Gene View AMD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN A 267 Homo sapiens EC#: 4.1.1.50 IUBMB
Mutation: S68X
Gene Name(s): AMD1 Gene View AMD

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

A METHYLGLYOXAL BIS-(GUANYLHYDRAZONE)
C5 H12 N8
MXWHMTNPTTVWDM-NXOFHUPFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PUT
Query on PUT

A 1,4-DIAMINOBUTANE
PUTRESCINE (Synonym)
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MGB N/A in BindingDB
IC50: 400 nM  BindingMOAD
IC50: 400 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PYR
Query on PYR
A NON-POLYMER C3 H4 O3 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.176
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 97.06 α = 90.00
b = 45.50 β = 105.24
c = 72.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-03-08
  • Released Date: 2001-08-22
  • Deposition author(s): Tolbert, W.D., Ekstrom, J.L., Mathews, I.I., Secrist III, J.A., Pegg, A.E., Ealick, S.E.

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