6YRT

Transaldolase variant T30D from T. acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate

PDB DOI: https://doi.org/10.2210/pdb6YRT/pdb

Classification: TRANSFERASE
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-04-20 Released: 2021-05-12
Deposition Author(s): Sautner, V., Klaus, M., Tittmann, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.187
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release

Sautner, V., Lietzow, T.H., Klaus, M., Funk, L.M., Tittmann, K.

To be published.

Macromolecule Content

Total Structure Weight: 124.82 kDa
Atom Count: 9,425
Modelled Residue Count: 1,097
Deposited Residue Count: 1,115
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transaldolase	A, B, C, D, E	223	Thermoplasma acidophilum DSM 1728	Mutation(s): 1 Gene Names: tal, Ta0616 EC: 2.2.1.2
UniProt
Find proteins for Q9HKI3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKI3 Go to UniProtKB: Q9HKI3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HKI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F6R (Subject of Investigation/LOI) Query on F6R Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E]	F [auth A], J [auth B], M [auth C], Q [auth D], S [auth E]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E]	G [auth A] H [auth A] K [auth B] N [auth C] O [auth C] G [auth A], H [auth A], K [auth B], N [auth C], O [auth C], R [auth D], T [auth E], U [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain V [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth E]	I [auth A], L [auth B], P [auth C], V [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain V [auth E] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain V [auth E]