3MTG | pdb_00003mtg

Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein

• PDB DOI: https://doi.org/10.2210/pdb3MTG/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-04-30 Released: 2010-05-26 
• Deposition Author(s): Wisniewska, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Persson, C., Schutz, P., Thorsell, A.G., Tresaugues, L., van der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Schuler, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.249 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein

Wisniewska, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Persson, C., Schutz, P., Thorsell, A.G., Tresaugues, L., van der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Schuler, H.

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.28 kDa 
• Atom Count: 6,792 
• Modelled Residue Count: 853 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative adenosylhomocysteinase 2	A, B	444	Homo sapiens	Mutation(s): 1  Gene Names: AHCYL1, DCAL, Irbit, XPVKONA EC: 3.3.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43865 (Homo sapiens) Explore O43865  Go to UniProtKB:  O43865
PHAROS:  O43865 GTEx:  ENSG00000168710

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.249 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.24	α = 90
b = 68.6	β = 115.27
c = 90.37	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Wisniewska, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Persson, C., Schutz, P., Thorsell, A.G., Tresaugues, L., van der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Schuler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description