2V4M | pdb_00002v4m

The isomerase domain of human glutamine-fructose-6-phosphate transaminase 1 (GFPT1) in complex with fructose 6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb2V4M/pdb

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


• Deposited: 2008-09-26 Released: 2008-10-07 
• Deposition Author(s): Moche, M., Lehtio, L., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Svensson, S., Schueler, H., Thorsell, A.G., Tresaugues, L., Uppenberg, J., Van Den Berg, S., Welin, M., Wisniewska, M., Weigelt, J., Nordlund, P., Wikstrom, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.185 (Depositor) 
• R-Value Work: 
  0.167 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

The Isomerase Domain of Human Gfpt1 in Complex with Fructose 6-Phosphate

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

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 PQS (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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 170.58 kDa 
• Atom Count: 11,333 
• Modeled Residue Count: 1,405 
• Deposited Residue Count: 1,504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1	A, B, C, D	376	Homo sapiens	Mutation(s): 0  EC: 2.6.1.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q06210 (Homo sapiens) Explore Q06210  Go to UniProtKB:  Q06210
PHAROS:  Q06210 GTEx:  ENSG00000198380

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F6R	E [auth A], F [auth B], G [auth C], I [auth D]	FRUCTOSE -6-PHOSPHATE C6 H13 O9 P GSXOAOHZAIYLCY-HSUXUTPPSA-N
CL	H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.185 (Depositor) 
• R-Value Work:  0.167 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.824	α = 90
b = 178.824	β = 90
c = 157.113	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Moche, M., Lehtio, L., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Svensson, S., Schueler, H., Thorsell, A.G., Tresaugues, L., Uppenberg, J., Van Den Berg, S., Welin, M., Wisniewska, M., Weigelt, J., Nordlund, P., Wikstrom, M.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description