1IID

Crystal Structure of Saccharomyces cerevisiae N-myristoyltransferase with Bound S-(2-oxo)pentadecylCoA and the Octapeptide GLYASKLA

Structural Biology Knowledgebase: 1IID SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.242

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1IID

Classification: TRANSFERASE

Total Structure Weight: 50946.88

Macromolecule Entities
Molecule Chains Length Organism Details
Peptide N-myristoyltransferase A 422 Saccharomyces cerevisiae EC#: 2.3.1.97 IUBMB
Fragment: N-myristoyltransferase (N-terminal 33 residues deleted)
Gene Name(s): NMT1 Gene View CDC72 YLR195C L8167.14
Octapeptide GLYASKLA O 8 synthetic

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

A S-(2-OXO)PENTADECYLCOA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-SXKLBCNJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.242
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 75.13 α = 90.00
b = 97.06 β = 90.00
c = 141.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-04-22
  • Released Date: 2001-05-02
  • Deposition author(s): Farazi, T.A., Gordon, J.I., Waksman, G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4