6DK3

HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2

• PDB DOI: https://doi.org/10.2210/pdb6DK3/pdb
• Entry: 6DK3 supersedes: 3OU5

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


• Deposited: 2018-05-28 Released: 2018-06-20 
• Deposition Author(s): Dong, A., Wu, H., Zeng, H., Loppnau, P., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.258 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2

Wu, H., Dong, A., Zeng, H., Loppnau, P., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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 (software)

Macromolecule Content

• Total Structure Weight: 54.11 kDa 
• Atom Count: 3,389 
• Modelled Residue Count: 423 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	A	488	Homo sapiens	Mutation(s): 0  Gene Names: SHMT2 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34897 (Homo sapiens) Explore P34897  Go to UniProtKB:  P34897
PHAROS:  P34897 GTEx:  ENSG00000182199

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.258 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.034	α = 90
b = 75.029	β = 108.77
c = 75.199	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Dong, A., Wu, H., Zeng, H., Loppnau, P., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)
• This entry supersedes: 3OU5

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description