8PA2 | pdb_00008pa2

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form

PDB DOI: https://doi.org/10.2210/pdb8PA2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-06-07 Released: 2024-06-26
Deposition Author(s): Rozeboom, H.J., Janssen, D.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (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

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form

Delgado-Arciniega, E., Bodescu, V., Rozeboom, H.J., Janssen, D.B., Wijma, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 115.83 kDa
Atom Count: 7,995
Modeled Residue Count: 995
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short-chain dehydrogenase/reductase family	A, B, C, D	264	Thermus thermophilus HB8	Mutation(s): 9 Gene Names: TTHA0369
UniProt
Find proteins for Q5SLC4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLC4 Go to UniProtKB: Q5SLC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SLC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B]	H [auth B], I [auth C], K [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]