6WKB | pdb_00006wkb

Human S-adenosylmethionine synthetase co-crystallized with UppNHp and Met

• PDB DOI: https://doi.org/10.2210/pdb6WKB/pdb

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


• Deposited: 2020-04-15 Released: 2021-04-21 
• Deposition Author(s): Tan, L.L., Jackson, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

S-adenosylmethionine synthetase

Laurino, P., Jackson, C.J., Tan, L.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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.26 kDa 
• Atom Count: 6,146 
• Modeled Residue Count: 761 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase isoform type-2	A, B	395	Homo sapiens	Mutation(s): 0  Gene Names: MAT2A, AMS2, MATA2 EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P31153 (Homo sapiens) Explore P31153  Go to UniProtKB:  P31153
PHAROS:  P31153 GTEx:  ENSG00000168906

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U4P	C [auth A], G [auth B]	5'-deoxyuridine C9 H12 N2 O5 WUBAOANSQGKRHF-XVFCMESISA-N
MET	F [auth B]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
MED	D [auth A]	D-METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-SCSAIBSYSA-N
EDO	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.191	α = 90
b = 144.191	β = 90
c = 188.196	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Tan, L.L., Jackson, C.J.

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description