8CIP | pdb_00008cip

Crystal structure of transketolase from Geobacillus stearothermophilus

PDB DOI: https://doi.org/10.2210/pdb8CIP/pdb

Classification: TRANSFERASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-10 Released: 2023-03-01
Deposition Author(s): Leogrande, C., Rabe von Pappenheim, F., Tittmann, K.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of transketolase from Geobacillus stearothermophilus

Leogrande, C., Rabe von Pappenheim, F., Tittman, K.

To be published.

Macromolecule Content

Total Structure Weight: 297.36 kDa
Atom Count: 20,989
Modeled Residue Count: 2,660
Deposited Residue Count: 2,724
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A, B, C, D	681	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: tkt EC: 2.2.1.1
UniProt
Find proteins for A0A0I9QGZ2 (Geobacillus stearothermophilus) Explore A0A0I9QGZ2 Go to UniProtKB: A0A0I9QGZ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0I9QGZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B]	FA [auth C], LA [auth D], M [auth A], U [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain FA [auth C] Focus chain LA [auth D] Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain FA [auth C] Focus chain LA [auth D] Focus chain M [auth A] Focus chain U [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] E [auth A] EA [auth C] AA [auth C], BA [auth C], CA [auth C], E [auth A], EA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], R [auth B], S [auth B], T [auth B], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain KA [auth D] SDF format, chain L [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A]	DA [auth C], KA [auth D], L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth C] Focus chain KA [auth D] Focus chain L [auth A] Interactions & Density Focus chain DA [auth C] Focus chain KA [auth D] Focus chain L [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain W [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B]	HA [auth C], O [auth A], P [auth A], Q [auth A], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Interactions & Density Focus chain HA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain V [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B]	GA [auth C], MA [auth D], N [auth A], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain GA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain V [auth B]