3IHL | pdb_00003ihl

Human CTPS2 crystal structure

• PDB DOI: https://doi.org/10.2210/pdb3IHL/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-30 Released: 2009-10-13 
• Deposition Author(s): Moche, 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, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Kragh Nielsen, T., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schueler, H., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Human CTPS2 crystal structure

Moche, 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, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Kragh Nielsen, T., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schueler, H., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.01 kDa 
• Atom Count: 3,686 
• Modeled Residue Count: 462 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTP synthase 2	A, B	282	Homo sapiens	Mutation(s): 0  Gene Names: CTPS2 EC: 6.3.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRF8 (Homo sapiens) Explore Q9NRF8  Go to UniProtKB:  Q9NRF8
PHAROS:  Q9NRF8 GTEx:  ENSG00000047230

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4	D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.25	α = 90
b = 168.25	β = 90
c = 132	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Moche, 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, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Kragh Nielsen, T., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schueler, H., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description