8XVN | pdb_00008xvn

Short-chain dehydrogenase/reductase6 (SDR6) from Antrodia camphorata

PDB DOI: https://doi.org/10.2210/pdb8XVN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Taiwanofungus camphoratus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-15 Released: 2025-01-15
Deposition Author(s): Zhang, Y.Q., Zhang, M., Ye, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.192 (Depositor), 0.193 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

[Not Available].

Zhang, Y.Q., Zhang, M., Wang, Z.L., Bao, Y.O., Wang, Y.Q., Tian, Y.G., Ye, L., Ye, M.

(2025) Angew Chem Int Ed Engl 64: e202420104-e202420104

PubMed: 39617723 Search on PubMed
DOI: https://doi.org/10.1002/anie.202420104
Primary Citation Related Structures:
8WZZ, 8XVN

PubMed Abstract:
Through different gene mining strategies, three key enzymes (AcCYP4, AcSDR6, AcSMT1) involved in the downstream biosynthesis of major lanostane-type triterpenoids were discovered and identified from Antrodia camphorata. The catalytic mechanisms of AcSDR6 were elucidated by crystal structure analysis. These post-modification enzymes could be used to synthesize at least 11 major Antrodia lanostanoids.

Organizational Affiliation

State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.

Macromolecule Content

Total Structure Weight: 227.59 kDa
Atom Count: 14,570
Modeled Residue Count: 1,821
Deposited Residue Count: 2,160
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenases/reductase	A, B, C, D, E A, B, C, D, E, F, G, H	270	Taiwanofungus camphoratus	Mutation(s): 0 EC: 1.1.1.100
UniProt
Find proteins for A0A165BBH9 (Laetiporus sulphureus 93-53) Explore A0A165BBH9 Go to UniProtKB: A0A165BBH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A165BBH9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.192 (Depositor), 0.193 (DCC)
R-Value Work: 0.164 (Depositor), 0.166 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.41	α = 90
b = 133.46	β = 91.03
c = 94.221	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release
Version 1.1: 2026-07-29
Changes: Database references

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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.