7BYI | pdb_00007byi

Structure of SHMT2 in complex with CBX

• PDB DOI: https://doi.org/10.2210/pdb7BYI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-04-23 Released: 2021-09-15 
• Deposition Author(s): Li, L., Chen, Y., Lu, D., Zhang, C., Su, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Structure of SHMT2 with CBX

Li, L., Su, D.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 108.14 kDa 
• Atom Count: 7,363 
• Modeled Residue Count: 925 
• Deposited Residue Count: 966 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	A	483	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	B	483	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CBO (Subject of Investigation/LOI)	E [auth B], F [auth B]	CARBENOXOLONE C34 H50 O7 OBZHEBDUNPOCJG-WBXJDKIVSA-N
PEG (Subject of Investigation/LOI)	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	C [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.62	α = 90
b = 158.62	β = 90
c = 209.427	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Li, L., Chen, Y., Lu, D., Zhang, C., Su, D.

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2021-12-01
  Changes: Database references, Structure summary
• Version 1.2: 2023-06-07
  Changes: Data collection
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description