2I6T

Orthorhombic Structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

• PDB DOI: https://doi.org/10.2210/pdb2I6T/pdb

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


• Deposited: 2006-08-29 Released: 2006-10-24 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty Jr., P.J., Butler-Cole, C., Tempel, W., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.230 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Structural Investigation into the L-lactate Dehydrogenase Domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

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

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 66.67 kDa 
• Atom Count: 4,673 
• Modelled Residue Count: 562 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A	A, B	303	Homo sapiens	Mutation(s): 0  Gene Names: UEVLD
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
SO4	C [auth A], D [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.230 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.088	α = 90
b = 98.912	β = 90
c = 126.753	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-24 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty Jr., P.J., Butler-Cole, C., Tempel, W., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

Revision History  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description