3IHJ | pdb_00003ihj

Human alanine aminotransferase 2 in complex with PLP

• PDB DOI: https://doi.org/10.2210/pdb3IHJ/pdb

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


• Deposited: 2009-07-30 Released: 2009-08-18 
• 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, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Moche, M., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Schutz, P., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Schuler, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Human glutamate pyruvate transaminase 2

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, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Moche, M., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Schutz, P., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.84 kDa 
• Atom Count: 3,696 
• Modeled Residue Count: 461 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine aminotransferase 2	A	498	Homo sapiens	Mutation(s): 0  Gene Names: GPT2, AAT2, ALT2 EC: 2.6.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TD30 (Homo sapiens) Explore Q8TD30  Go to UniProtKB:  Q8TD30
PHAROS:  Q8TD30 GTEx:  ENSG00000166123

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.73	α = 90
b = 92.73	β = 90
c = 262.87	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: 2009-08-18 
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, A., Johansson, I., Karlberg, T., Kotenyova, T., Kotzsch, A., Moche, M., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Schutz, P., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Schuler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-01-15
  Changes: Advisory, Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description