8T0Q | pdb_00008t0q

Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

PDB DOI: https://doi.org/10.2210/pdb8T0Q/pdb
EM Map EMD-40945: EMDB EMDataResource

Classification: ISOMERASE
Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-01 Released: 2024-07-03
Deposition Author(s): Tian, S., Voss, P., Pham, K., Klose, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Catalysis in Motion: Large-Scale Domain Shift Enables Co-C Bond Homolysis in Lysine 5,6-Aminomutase

Tian, S., Voss, P., Pham, K., Toba, D., Liu, M., Das, N., Yachuw, S., Denault, C., Klose, T., Uyeda, C.

To be published.

Macromolecule Content

Total Structure Weight: 182.5 kDa
Atom Count: 12,355
Modelled Residue Count: 1,547
Deposited Residue Count: 1,602
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lysine 5,6-aminomutase beta subunit	A, B	269	Caldanaerobacter subterraneus subsp. tengcongensis	Mutation(s): 0 Gene Names: TTE0727
UniProt
Find proteins for Q8RBT2 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBT2 Go to UniProtKB: Q8RBT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RBT2
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lysine 5,6-aminomutase alpha subunit	C, D	532	Caldanaerobacter subterraneus subsp. tengcongensis	Mutation(s): 0 Gene Names: TTE0726
UniProt
Find proteins for Q8RBT3 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBT3 Go to UniProtKB: Q8RBT3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RBT3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
5AD (Subject of Investigation/LOI) Query on 5AD Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	I [auth C], J [auth D]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain I [auth C] Focus chain J [auth D]
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]