8U09

Crystal structure of substrate-free SyoA

PDB DOI: https://doi.org/10.2210/pdb8U09/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amycolatopsis thermoflava N1165
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-28 Released: 2024-07-24
Deposition Author(s): Harlington, A.H., Shearwin, K.E., Bell, S.G., Whelan, F.
Funding Organization(s): Wine Australia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.205
R-Value Work: 0.172
R-Value Observed: 0.174

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

Structural insights into the S-lignin O-demethylase SyoA

Harlington, A.H., Shearwin, K.E., Bell, S.G., Whelan, F.

To be published.

Macromolecule Content

Total Structure Weight: 46.76 kDa
Atom Count: 3,511
Modelled Residue Count: 392
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	412	Amycolatopsis thermoflava N1165	Mutation(s): 0 EC: 1.14.14.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]