3DAX | pdb_00003dax

Crystal structure of human CYP7A1

• PDB DOI: https://doi.org/10.2210/pdb3DAX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-05-30 Released: 2008-08-05 
• Deposition Author(s): Strushkevich, N.V., Tempel, W., Dombrovski, L., Dong, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human CYP7A1

Strushkevich, N.V., Tempel, W., Dombrovski, L., Dong, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.17 kDa 
• Atom Count: 7,737 
• Modelled Residue Count: 942 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 7A1	A, B	491	Homo sapiens	Mutation(s): 0  Gene Names: CYP7A1, CYP7 EC: 1.14.13.17 (PDB Primary Data), 1.14.14.26 (UniProt), 1.14.14.23 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P22680 (Homo sapiens) Explore P22680  Go to UniProtKB:  P22680
PHAROS:  P22680 GTEx:  ENSG00000167910

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
UNX	D [auth A], F [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33dax

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.339	α = 64.36
b = 80.159	β = 75.23
c = 84.937	γ = 72.17

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Strushkevich, N.V., Tempel, W., Dombrovski, L., Dong, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2020-10-21
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description