8K32 | pdb_00008k32

The complex structure of SLKARI with NADH at 2.12-angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8K32/pdb

Classification: OXIDOREDUCTASE
Organism(s): Syntrophothermus lipocalidus DSM 12680
Expression System: Expression vector pET-mod
Mutation(s): No

Deposited: 2023-07-14 Released: 2024-07-17
Deposition Author(s): Chen, C.Y., Huang, C.H.
Funding Organization(s): National Key Basic Research Program of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural bases of coenzyme specificity of thermophilic ketol-acid reductoisomerase

Chen, C.Y., Huang, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 152.04 kDa
Atom Count: 11,652
Modeled Residue Count: 1,329
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+))	A, B, C, D	334	Syntrophothermus lipocalidus DSM 12680	Mutation(s): 0 Gene Names: ilvC, Slip_2160 EC: 1.1.1.86
UniProt
Find proteins for D7CJ24 (Syntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)) Explore D7CJ24 Go to UniProtKB: D7CJ24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D7CJ24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain P [auth B] SDF format, chain HA [auth D] SDF format, chain E [auth A] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain E [auth A]	E [auth A], HA [auth D], P [auth B], X [auth C]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth D] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain HA [auth D] Focus chain P [auth B] Focus chain X [auth C]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain O [auth A] MOL2 format, chain W [auth B] MOL2 format, chain O [auth A] mmCIF format, chain W [auth B] mmCIF format, chain O [auth A]	O [auth A], W [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain O [auth A] Focus chain W [auth B] Interactions & Density Focus chain O [auth A] Focus chain W [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain NA [auth D] SDF format, chain MA [auth D] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] F [auth A] G [auth A] AA [auth C], BA [auth C], CA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], LA [auth D], MA [auth D], NA [auth D], Q [auth B], R [auth B], S [auth B], T [auth B], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain GA [auth C] SDF format, chain FA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C]	FA [auth C], GA [auth C], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain N [auth A] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain N [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain PA [auth D] SDF format, chain OA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain EA [auth C] SDF format, chain DA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C]	DA [auth C] EA [auth C] L [auth A] M [auth A] OA [auth D] DA [auth C], EA [auth C], L [auth A], M [auth A], OA [auth D], PA [auth D], U [auth B], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B]