3DL2 | pdb_00003dl2

Hexagonal structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

• PDB DOI: https://doi.org/10.2210/pdb3DL2/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-26 Released: 2008-07-15 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty Jr., P.J., Butler-Cole, C., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structural Investigation Into the L-Lactate Dehydrogenase Domain of Human Ubiquitin-Conjugating Enzyme E2-Like Isoform A.

Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty Jr., P.J., Butler-Cole, C., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

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: 65.97 kDa 
• Atom Count: 4,574 
• Modeled Residue Count: 576 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 variant 3	A, B	303	Homo sapiens	Mutation(s): 0  Gene Names: UEVLD, UEV3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IX04 (Homo sapiens) Explore Q8IX04  Go to UniProtKB:  Q8IX04
PHAROS:  Q8IX04 GTEx:  ENSG00000151116

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], F [auth B], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.603	α = 90
b = 105.603	β = 90
c = 131.918	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty Jr., P.J., Butler-Cole, C., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description