6RNG | pdb_00006rng

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

PDB DOI: https://doi.org/10.2210/pdb6RNG/pdb

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

Deposited: 2019-05-08 Released: 2020-04-15
Deposition Author(s): Shahar, A., Zarivach, R., Skirycz, A., Wojciechowska, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.296 (Depositor), 0.295 (DCC)
R-Value Work:
0.243 (Depositor), 0.247 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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.

Not Published

Macromolecule Content

Total Structure Weight: 155.55 kDa
Atom Count: 10,669
Modeled Residue Count: 1,342
Deposited Residue Count: 1,432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase 6, cytosolic	A, B, C [auth F], D [auth G]	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRO Query on PRO Download:Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain U [auth G] SDF format, chain M [auth B] MOL2 format, chain W [auth G] MOL2 format, chain U [auth G] MOL2 format, chain M [auth B] mmCIF format, chain W [auth G] mmCIF format, chain U [auth G] mmCIF format, chain M [auth B]	M [auth B], U [auth G], W [auth G]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain M [auth B] Focus chain U [auth G] Focus chain W [auth G] Interactions & Density Focus chain M [auth B] Focus chain U [auth G] Focus chain W [auth G]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth G] SDF format, chain R [auth G] SDF format, chain Q [auth G] SDF format, chain P [auth G] SDF format, chain O [auth F] SDF format, chain N [auth F] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth G] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth G] MOL2 format, chain O [auth F] MOL2 format, chain N [auth F] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth G] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth G] mmCIF format, chain O [auth F] mmCIF format, chain N [auth F] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth B] G [auth B] H [auth B] I [auth B] E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], N [auth F], O [auth F], P [auth G], Q [auth G], R [auth G], S [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain V [auth G] SDF format, chain T [auth G] SDF format, chain L [auth B] MOL2 format, chain V [auth G] MOL2 format, chain T [auth G] MOL2 format, chain L [auth B] mmCIF format, chain V [auth G] mmCIF format, chain T [auth G] mmCIF format, chain L [auth B]	L [auth B], T [auth G], V [auth G]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth G] Focus chain V [auth G] Interactions & Density Focus chain L [auth B] Focus chain T [auth G] Focus chain V [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.296 (Depositor), 0.295 (DCC)
R-Value Work: 0.243 (Depositor), 0.247 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.399	α = 90
b = 73.164	β = 106.52
c = 176.225	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2020-10-28
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description