3E04

Crystal structure of human fumarate hydratase

• PDB DOI: https://doi.org/10.2210/pdb3E04/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-30 Released: 2008-08-12 
• Deposition Author(s): Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.244 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Crystal structure of human fumarate hydratase

Kavanagh, K.L., Picaud, S., Pilka, E.S., Yue, W.W., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 212.03 kDa 
• Atom Count: 13,827 
• Modelled Residue Count: 1,784 
• Deposited Residue Count: 1,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase	A, B, C, D	490	Homo sapiens	Mutation(s): 0  Gene Names: FH EC: 4.2.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07954 (Homo sapiens) Explore P07954  Go to UniProtKB:  P07954
PHAROS:  P07954 GTEx:  ENSG00000091483

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.244 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.483	α = 90
b = 188.483	β = 90
c = 114.632	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-12-05
  Changes: Database references
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description