1I7M

HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.242

Literature

Macromolecules
Sequence Display for 1I7M

Classification: LYASE

Total Structure Weight: 78496.05

Macromolecule Entities
Molecule Chains Length Organism Details
S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN B, D 67 Homo sapiens EC#: 4.1.1.50 IUBMB
Mutation: M1M
Gene Name(s): AMD1 Gene View AMD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN A, C 267 Homo sapiens EC#: 4.1.1.50 IUBMB
Mutation: S68X, M70M, M118M, M149M, M152M, M181M, M189M, M194M, M222M, M230M, M233M, M314M
Gene Name(s): AMD1 Gene View AMD

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

A, D 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE
C11 H14 N6
CYPGNVSXMAUSJY-CXUHLZMHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PUT
Query on PUT

B, D 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 %)
CG IC50: 5 nM (95) BindingDB

IC50: 0.23 nM  BindingMOAD
N/A in PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET
PYR
Query on PYR
A, C NON-POLYMER C3 H4 O3 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.242
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 73.90 α = 90.00
b = 55.67 β = 110.39
c = 96.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-03-09
  • 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