8YXY | pdb_00008yxy

NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of Imine Reductase Mutant(M6) from Pochonia chlamydosporia 170

PDB DOI: https://doi.org/10.2210/pdb8YXY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pochonia chlamydosporia 170
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-03 Released: 2025-07-09
Deposition Author(s): Shi, M., Zheng, G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.176 (Depositor), 0.182 (DCC)
R-Value Work:
0.154 (Depositor), 0.163 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: in silico
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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

NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of Imine Reductase wild type from Pochonia chlamydosporia 170

Shi, M., Zheng, G.

To be published.

Macromolecule Content

Total Structure Weight: 63.21 kDa
Atom Count: 5,050
Modeled Residue Count: 577
Deposited Residue Count: 586
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	A, B	293	Pochonia chlamydosporia 170	Mutation(s): 0 Gene Names: VFPPC_03305
UniProt
Find proteins for A0A179FZ20 (Pochonia chlamydosporia 170) Explore A0A179FZ20 Go to UniProtKB: A0A179FZ20
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A179FZ20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
A1D7O (Subject of Investigation/LOI) Query on A1D7O Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	(4~{R})-4-methyl-1-(phenylmethyl)piperidin-3-one C₁₃ H₁₇ N O BSBVJNUGGBQEPO-LLVKDONJSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]