8RPJ

JanthE from Janthinobacterium sp. HH01

PDB DOI: https://doi.org/10.2210/pdb8RPJ/pdb

Classification: TRANSFERASE
Organism(s): Janthinobacterium sp. HH01
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-16 Released: 2024-06-12
Deposition Author(s): Lanza, L., Leogrande, C., Rabe von Pappenheim, F., Tittmann, K., Mueller, M.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.186
R-Value Work: 0.153
R-Value Observed: 0.155

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

JhE from Janthinobacterium sp. HH01

Lanza, L., Leogrande, C., Rabe von Pappenheim, F.

To be published.

Macromolecule Content

Total Structure Weight: 416.8 kDa
Atom Count: 30,592
Modelled Residue Count: 3,617
Deposited Residue Count: 3,714
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine pyrophosphate-binding protein	A, B, C, D, E A, B, C, D, E, F	619	Janthinobacterium sp. HH01	Mutation(s): 0 EC: 2.2.1.6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E]	EA [auth F] H [auth A] K [auth B] R [auth C] V [auth D] EA [auth F], H [auth A], K [auth B], R [auth C], V [auth D], Y [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain EA [auth F] Focus chain H [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain EA [auth F] Focus chain H [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E]
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E]	DA [auth F] G [auth A] J [auth B] Q [auth C] U [auth D] DA [auth F], G [auth A], J [auth B], Q [auth C], U [auth D], X [auth E]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain DA [auth F] Focus chain G [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain DA [auth F] Focus chain G [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C]	T [auth C]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain M [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain M [auth B]	AA [auth E], M [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain M [auth B] Interactions & Density Focus chain AA [auth E] Focus chain M [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth E] MOL2 format, chain CA [auth E]	CA [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Interactions & Density Focus chain CA [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain GA [auth F] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain BA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	BA [auth E], GA [auth F], N [auth B], O [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain GA [auth F] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth F] Focus chain N [auth B] Focus chain O [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E]	FA [auth F] I [auth A] L [auth B] S [auth C] W [auth D] FA [auth F], I [auth A], L [auth B], S [auth C], W [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth F] Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain FA [auth F] Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E]