3ELB | pdb_00003elb

Human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CMP

• PDB DOI: https://doi.org/10.2210/pdb3ELB/pdb

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


• Deposited: 2008-09-22 Released: 2008-10-21 
• Deposition Author(s): Karlberg, T., Welin, M., Andersson, J., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wikstrom, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Human CTP:Phosphoethanolamine Cytidylyltransferase

Karlberg, T., Welin, M., Andersson, J., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wikstrom, M., Wisniewska, M., Schuler, H.

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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.53 kDa 
• Atom Count: 2,657 
• Modeled Residue Count: 302 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine-phosphate cytidylyltransferase	A	341	Homo sapiens	Mutation(s): 0  Gene Names: PCYT2 EC: 2.7.7.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q99447 (Homo sapiens) Explore Q99447  Go to UniProtKB:  Q99447
PHAROS:  Q99447 GTEx:  ENSG00000185813

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5P	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.179	α = 90
b = 74.179	β = 90
c = 139.723	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SHELXS	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Karlberg, T., Welin, M., Andersson, J., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wikstrom, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary