2V4M

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

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
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06210
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F6R Query on F6R Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D]	E [auth A], F [auth B], G [auth C], I [auth D]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain I [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C]	H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.185
R-Value Work: 0.167
R-Value Observed: 0.168
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

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

2V4M

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)