6RS1 | pdb_00006rs1

Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase

PDB DOI: https://doi.org/10.2210/pdb6RS1/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2019-05-21 Released: 2020-04-01
Deposition Author(s): Shahar, A., Zarivach, R., Skirycz, A., Wojciechowska, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.254 (Depositor), 0.265 (DCC)
R-Value Work:
0.214 (Depositor), 0.228 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RS1

This is version 1.1 of the entry. See complete history.

Literature

Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase

Wojciechowska, I., Vogeli, B., Shahar, A., Szlachetko, J., Gorka, M., Sokolowska, E.M., Veyel, D., Silva, D.V., Erb, T., Zarivach, R., Skirycz, A.

To be published.

Macromolecule Content

Total Structure Weight: 154.6 kDa
Atom Count: 10,957
Modeled Residue Count: 1,348
Deposited Residue Count: 1,432
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase 6, cytosolic	A, B, C, D	358	Arabidopsis thaliana	Mutation(s): 0 Gene Names: FBA6, At2g36460 EC: 4.1.2.13
UniProt
Find proteins for Q9SJQ9 (Arabidopsis thaliana) Explore Q9SJQ9 Go to UniProtKB: Q9SJQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SJQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth B] E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.254 (Depositor), 0.265 (DCC)
R-Value Work: 0.214 (Depositor), 0.228 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.567	α = 79.95
b = 67.636	β = 73.13
c = 88.908	γ = 65.58

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Wojciechowska, I.

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.