8UAS | pdb_00008uas

Rhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex - Compound 1a

PDB DOI: https://doi.org/10.2210/pdb8UAS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus ruber
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-22 Released: 2024-07-03
Deposition Author(s): Wilson, L.A., Guddat, L.W., Schenk, G., Scott, C.
Funding Organization(s): Commonwealth Scientific and Industrial Research Organisation (CSIRO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8UAS

Ligand Structure Quality Assessment

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

Literature

Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics

Rocha, R.A., Wilson, L.A., Schwartz, B.D., Warden, A.C., Guddat, L.W., Speight, R.E., Malins, L., Schenk, G., Scott, C.

(2024) Catalysts 14

DOI: https://doi.org/10.3390/catal14070399

Macromolecule Content

Total Structure Weight: 453.94 kDa
Atom Count: 32,483
Modeled Residue Count: 4,189
Deposited Residue Count: 4,380
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodococcus ruber Alcohol Dehydrogenase Chain A	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	365	Rhodococcus ruber	Mutation(s): 0 EC: 1.1.1.1
UniProt
Find proteins for A0AAT8XUI2 (Rhodococcus ruber) Explore A0AAT8XUI2 Go to UniProtKB: A0AAT8XUI2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAT8XUI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W3O (Subject of Investigation/LOI) Query on W3O Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain EA [auth E] SDF format, chain IA [auth F] SDF format, chain MA [auth G] SDF format, chain V [auth C] SDF format, chain YA [auth J] SDF format, chain UA [auth I] SDF format, chain PA [auth H] SDF format, chain DB [auth L] SDF format, chain CB [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain YA [auth J] MOL2 format, chain UA [auth I] MOL2 format, chain PA [auth H] MOL2 format, chain DB [auth L] MOL2 format, chain CB [auth K] mmCIF format, chain AA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain YA [auth J] mmCIF format, chain UA [auth I] mmCIF format, chain PA [auth H] mmCIF format, chain DB [auth L] mmCIF format, chain CB [auth K]	AA [auth D] CB [auth K] DB [auth L] EA [auth E] IA [auth F] AA [auth D], CB [auth K], DB [auth L], EA [auth E], IA [auth F], MA [auth G], PA [auth H], UA [auth I], V [auth C], YA [auth J]	1-[3-[~{tert}-butyl(dimethyl)silyl]oxypropyl]pyridine-3-carboxamide C₁₅ H₂₇ N₂ O₂ Si IGAWBMMYKICDLH-UHFFFAOYSA-O		Interactions Focus chain AA [auth D] Focus chain CB [auth K] Focus chain DB [auth L] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain MA [auth G] Focus chain PA [auth H] Focus chain UA [auth I] Focus chain V [auth C] Focus chain YA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain CB [auth K] Focus chain DB [auth L] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain MA [auth G] Focus chain PA [auth H] Focus chain UA [auth I] Focus chain V [auth C] Focus chain YA [auth J]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain RA [auth I] MOL2 format, chain RA [auth I] mmCIF format, chain RA [auth I]	RA [auth I]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain RA [auth I] Interactions & Density Focus chain RA [auth I]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain DA [auth E] SDF format, chain FB [auth L] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain NA [auth H] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain SA [auth I] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain XA [auth J] SDF format, chain WA [auth J] SDF format, chain TA [auth I] SDF format, chain OA [auth H] SDF format, chain N [auth A] SDF format, chain EB [auth L] SDF format, chain CA [auth E] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain DA [auth E] MOL2 format, chain FB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth J] MOL2 format, chain WA [auth J] MOL2 format, chain TA [auth I] MOL2 format, chain OA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain EB [auth L] MOL2 format, chain CA [auth E] mmCIF format, chain AB [auth K] mmCIF format, chain BB [auth K] mmCIF format, chain DA [auth E] mmCIF format, chain FB [auth L] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth I] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth J] mmCIF format, chain WA [auth J] mmCIF format, chain TA [auth I] mmCIF format, chain OA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain EB [auth L] mmCIF format, chain CA [auth E]	AB [auth K] BB [auth K] CA [auth E] DA [auth E] EB [auth L] AB [auth K], BB [auth K], CA [auth E], DA [auth E], EB [auth L], FB [auth L], GA [auth F], HA [auth F], KA [auth G], LA [auth G], N [auth A], NA [auth H], O [auth A], OA [auth H], Q [auth B], R [auth B], SA [auth I], T [auth C], TA [auth I], U [auth C], WA [auth J], XA [auth J], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth I] Focus chain T [auth C] Focus chain TA [auth I] Focus chain U [auth C] Focus chain WA [auth J] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth I] Focus chain T [auth C] Focus chain TA [auth I] Focus chain U [auth C] Focus chain WA [auth J] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain Z [auth D]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain JA [auth G] SDF format, chain QA [auth I] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain M [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain QA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain QA [auth I] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain M [auth A]	FA [auth F] JA [auth G] M [auth A] QA [auth I] S [auth C] FA [auth F], JA [auth G], M [auth A], QA [auth I], S [auth C], W [auth D], X [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain FA [auth F] Focus chain JA [auth G] Focus chain M [auth A] Focus chain QA [auth I] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain FA [auth F] Focus chain JA [auth G] Focus chain M [auth A] Focus chain QA [auth I] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain ZA [auth J] SDF format, chain VA [auth I] SDF format, chain P [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain ZA [auth J] MOL2 format, chain VA [auth I] MOL2 format, chain P [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain ZA [auth J] mmCIF format, chain VA [auth I] mmCIF format, chain P [auth A]	BA [auth D], P [auth A], VA [auth I], ZA [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain P [auth A] Focus chain VA [auth I] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain P [auth A] Focus chain VA [auth I] Focus chain ZA [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.210 (Depositor), 0.209 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.144	α = 90
b = 157.745	β = 91.06
c = 272.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Commonwealth Scientific and Industrial Research Organisation (CSIRO)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2024-07-03
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.