8UAR

Rhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex - Compound 4b

PDB DOI: https://doi.org/10.2210/pdb8UAR/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., Schenk, G., Guddat, L.W., Scott, C.
Funding Organization(s): Commonwealth Scientific and Industrial Research Organisation (CSIRO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.246
R-Value Work: 0.193
R-Value Observed: 0.194

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 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: 453.99 kDa
Atom Count: 30,414
Modelled Residue Count: 4,194
Deposited Residue Count: 4,380
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodococcus ruber ADH	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	365	Rhodococcus ruber	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W46 (Subject of Investigation/LOI) Query on W46 Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain LA [auth H] SDF format, chain O [auth A] SDF format, chain PA [auth I] SDF format, chain S [auth B] SDF format, chain SA [auth J] SDF format, chain W [auth C] SDF format, chain WA [auth K] SDF format, chain Z [auth D] MOL2 format, chain AB [auth L] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth K] MOL2 format, chain Z [auth D]	AB [auth L] CA [auth E] FA [auth F] LA [auth H] O [auth A] AB [auth L], CA [auth E], FA [auth F], LA [auth H], O [auth A], PA [auth I], S [auth B], SA [auth J], W [auth C], WA [auth K], Z [auth D]	1-{[4-(hydroxymethyl)phenyl]methyl}-1,4-dihydropyridine-3-carboxamide C₁₄ H₁₆ N₂ O₂ ICSSJCKDRDSOOW-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain LA [auth H] Focus chain O [auth A] Focus chain PA [auth I] Focus chain S [auth B] Focus chain SA [auth J] Focus chain W [auth C] Focus chain WA [auth K] Focus chain Z [auth D] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain LA [auth H] Focus chain O [auth A] Focus chain PA [auth I] Focus chain S [auth B] Focus chain SA [auth J] Focus chain W [auth C] Focus chain WA [auth K] Focus chain Z [auth D]
CIT (Subject of Investigation/LOI) Query on CIT Download Ideal Coordinates CCD File SDF format, chain KA [auth H] SDF format, chain OA [auth I] SDF format, chain R [auth B] SDF format, chain TA [auth K] SDF format, chain ZA [auth L] MOL2 format, chain KA [auth H] MOL2 format, chain OA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain ZA [auth L]	KA [auth H], OA [auth I], R [auth B], TA [auth K], ZA [auth L]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain KA [auth H] Focus chain OA [auth I] Focus chain R [auth B] Focus chain TA [auth K] Focus chain ZA [auth L] Interactions & Density Focus chain KA [auth H] Focus chain OA [auth I] Focus chain R [auth B] Focus chain TA [auth K] Focus chain ZA [auth L]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain NA [auth I] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth J] SDF format, chain RA [auth J] SDF format, chain U [auth C] SDF format, chain UA [auth K] SDF format, chain V [auth C] SDF format, chain VA [auth K] SDF format, chain X [auth D] SDF format, chain XA [auth L] SDF format, chain Y [auth D] SDF format, chain YA [auth L] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain RA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth K] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth L]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] GA [auth G] AA [auth E], BA [auth E], DA [auth F], EA [auth F], GA [auth G], HA [auth G], IA [auth H], JA [auth H], M [auth A], MA [auth I], N [auth A], NA [auth I], P [auth B], Q [auth B], QA [auth J], RA [auth J], U [auth C], UA [auth K], V [auth C], VA [auth K], X [auth D], XA [auth L], Y [auth D], YA [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain U [auth C] Focus chain UA [auth K] Focus chain V [auth C] Focus chain VA [auth K] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain YA [auth L] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain U [auth C] Focus chain UA [auth K] Focus chain V [auth C] Focus chain VA [auth K] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain YA [auth L]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]