1Z10

Crystal Structure of Human Microsomal P450 2A6 with Coumarin Bound

Structural Biology Knowledgebase: 1Z10 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Z10

Classification: OXIDOREDUCTASE

Total Structure Weight: 221831.66

Macromolecule Entities
Molecule Chains Length Organism Details
cytochrome P450, family 2, subfamily A, polypeptide 6 A, B, C, D 476 Homo sapiens EC#: 1.14.13 IUBMB
Fragment: catalytic domain
Gene Name(s): CYP2A6 Gene View CYP2A3

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

A, B, C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
COU
Query on COU

A, B, C, D COUMARIN
2H-1-BENZOPYRAN-2-ONE (Synonym)
C9 H6 O2
ZYGHJZDHTFUPRJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
COU N/A in BindingDB
Kd: 270 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.194
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.61 α = 90.00
b = 157.59 β = 92.25
c = 103.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-03-02
  • Released Date: 2005-08-16
  • Deposition author(s): Yano, J.K., Hsu, M.H., Griffin, K.J., Stout, C.D., Johnson, E.F.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4