6JML | pdb_00006jml

Re-refined structure of R-state L-lactate dehydrogenase fromLactobacillus casei

PDB DOI: https://doi.org/10.2210/pdb6JML/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lacticaseibacillus casei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-12 Released: 2020-05-06
Deposition Author(s): Arai, K., Miyanaga, A., Uchikoba, H., Fushinobu, S., Taguchi, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.222 (Depositor), 0.230 (DCC)
R-Value Work:
0.194 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of penta mutant of L-lactate dehydrogenase from Lactobacillus casei

Arai, K., Miyanaga, A., Uchikoba, H., Fushinobu, S., Taguchi, H.

To be published.

Macromolecule Content

Total Structure Weight: 214.58 kDa
Atom Count: 14,535
Modeled Residue Count: 1,853
Deposited Residue Count: 1,956
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B, C, D, E A, B, C, D, E, F	326	Lacticaseibacillus casei	Mutation(s): 0 Gene Names: ldh EC: 1.1.1.27
UniProt
Find proteins for P00343 (Lacticaseibacillus casei) Explore P00343 Go to UniProtKB: P00343
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]