5TD9 | pdb_00005td9

Structure of Human Enolase 2

• PDB DOI: https://doi.org/10.2210/pdb5TD9/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-19 Released: 2017-09-27 
• Deposition Author(s): Leonard, P.G., Muller, F.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Pomhex, a cell-permeable Enolase inhibitor for Collateral Lethality targeting of ENO1-deleted Glioblastoma

Lin, Y.H., Satani, N., Hammoudi, N., Felini, F., Leonard, P.G., Maxwell, D., Peng, Z., Link, T.M., Lee, G.R., Bosajou, A., Sun, D., Marszalek, J.R., Sun, Y.T., McMurray, J., Mandal, P.J., Zielinski, R., Priebe, W., DiFrancesco, M.E., Czako, B., Wang, Y.A., Bornmann, W., DePinho, R.A., Muller, F.L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 96.42 kDa 
• Atom Count: 6,734 
• Modeled Residue Count: 868 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-enolase	A, B	440	Homo sapiens	Mutation(s): 0  Gene Names: ENO2 EC: 4.2.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09104 (Homo sapiens) Explore P09104  Go to UniProtKB:  P09104
PHAROS:  P09104 GTEx:  ENSG00000111674

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.319	α = 90
b = 112.868	β = 90
c = 119.922	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data processing
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Leonard, P.G., Muller, F.L.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description