6NAK | pdb_00006nak

BACTERIAL PROTEIN COMPLEX TM BDE complex

PDB DOI: https://doi.org/10.2210/pdb6NAK/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-05 Released: 2023-04-26
Deposition Author(s): Stec, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free:
0.302 (Depositor), 0.299 (DCC)
R-Value Work:
0.192 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6FPE

Literature

Discovery of the Universal tRNA Binding Mode for the TsaD-like Components of the t6A tRNA Modification Pathway

Stec, B.

(2023) Biophysica 3: 288-306

DOI: https://doi.org/10.3390/biophysica3020019

Macromolecule Content

Total Structure Weight: 162.59 kDa
Atom Count: 10,983
Modeled Residue Count: 1,383
Deposited Residue Count: 1,434
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB	A, D [auth C]	206	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: tsaB, TM_0874, Tmari_0876
UniProt
Find proteins for Q9WZX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZX7 Go to UniProtKB: Q9WZX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZX7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA N6-adenosine threonylcarbamoyltransferase	B, E [auth G]	327	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: tsaD, gcp, TM_0145 EC: 2.3.1.234
UniProt
Find proteins for Q9WXZ2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXZ2 Go to UniProtKB: Q9WXZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WXZ2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TsaE	C [auth D], F [auth E]	184	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TsaE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC Query on APC Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain J [auth D] MOL2 format, chain N [auth E] MOL2 format, chain J [auth D] mmCIF format, chain N [auth E] mmCIF format, chain J [auth D]	J [auth D], N [auth E]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain J [auth D] Focus chain N [auth E] Interactions & Density Focus chain J [auth D] Focus chain N [auth E]
TXA Query on TXA Download:Ideal Coordinates CCD File SDF format, chain K [auth G] SDF format, chain G [auth B] MOL2 format, chain K [auth G] MOL2 format, chain G [auth B] mmCIF format, chain K [auth G] mmCIF format, chain G [auth B]	G [auth B], K [auth G]	threonylcarbamoyladenylate C₁₅ H₂₁ N₆ O₁₁ P GHLUPQUHEIJRCU-DWVDDHQFSA-N		Interactions Focus chain G [auth B] Focus chain K [auth G] Interactions & Density Focus chain G [auth B] Focus chain K [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain H [auth B] MOL2 format, chain L [auth G] MOL2 format, chain H [auth B] mmCIF format, chain L [auth G] mmCIF format, chain H [auth B]	H [auth B], L [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain L [auth G] Interactions & Density Focus chain H [auth B] Focus chain L [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain I [auth D] MOL2 format, chain M [auth E] MOL2 format, chain I [auth D] mmCIF format, chain M [auth E] mmCIF format, chain I [auth D]	I [auth D], M [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain M [auth E] Interactions & Density Focus chain I [auth D] Focus chain M [auth E]