8RPI

JanthE from Janthinobacterium sp. HH01, lactyl-ThDP

PDB DOI: https://doi.org/10.2210/pdb8RPI/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: 2.71 Å
R-Value Free: 0.234
R-Value Work: 0.195
R-Value Observed: 0.197

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: 416.38 kDa
Atom Count: 28,772
Modelled Residue Count: 3,629
Deposited Residue Count: 3,714
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F]	G [auth A] J [auth B] N [auth C] Q [auth D] T [auth E] G [auth A], J [auth B], N [auth C], Q [auth D], T [auth E], W [auth F]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F]
TDL (Subject of Investigation/LOI) Query on TDL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F]	I [auth A] M [auth B] P [auth C] S [auth D] V [auth E] I [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM C₁₅ H₂₃ N₄ O₁₀ P₂ S TVDSMGSBVYONNB-OAHLLOKOSA-O		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F]	H [auth A] K [auth B] O [auth C] R [auth D] U [auth E] H [auth A], K [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]