3E77 | pdb_00003e77

Human phosphoserine aminotransferase in complex with PLP

• PDB DOI: https://doi.org/10.2210/pdb3E77/pdb

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


• Deposited: 2008-08-18 Released: 2008-08-26 
• Deposition Author(s): Lehtio, L., Karlberg, T., 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., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Thorsell, S.G., Tresaugues, L., Van Den Berg, S., Welin, M., Wikstrom, M., Wisniewska, M., Weigelt, J., Schueler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Human phosphoserine aminotransferase in complex with PLP

Lehtio, L., Karlberg, T., 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., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Thorsell, S.G., Tresaugues, L., Van Den Berg, S., Welin, M., Wikstrom, M., Wisniewska, M., Weigelt, J., Schueler, H., Structural Genomics Consortium (SGC)

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 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: 125.05 kDa 
• Atom Count: 8,536 
• Modeled Residue Count: 1,087 
• Deposited Residue Count: 1,131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine aminotransferase	A, B, C	377	Homo sapiens	Mutation(s): 0  Gene Names: PSAT1, PSA EC: 2.6.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y617 (Homo sapiens) Explore Q9Y617  Go to UniProtKB:  Q9Y617
PHAROS:  Q9Y617 GTEx:  ENSG00000135069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171	α = 90
b = 171	β = 90
c = 103.88	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Lehtio, L., Karlberg, T., 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., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Thorsell, S.G., Tresaugues, L., Van Den Berg, S., Welin, M., Wikstrom, M., Wisniewska, M., Weigelt, J., Schueler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description