9FFE | pdb_00009ffe

Carbohydrate active oxidoreductases from Phytophthora sojae

PDB DOI: https://doi.org/10.2210/pdb9FFE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Phytophthora sojae
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2024-05-23 Released: 2025-03-12
Deposition Author(s): Banerjee, S., Turella, S., Morth, J.P., Abou Hachem, M.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.226 (Depositor), 0.228 (DCC)
R-Value Work:
0.174 (Depositor), 0.176 (DCC)
R-Value Observed:
0.176 (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

Carbohydrate active oxidoreductases from Phytophthora sojae

Turella, S., Banerjee, S., Morth, J.P., Abou Hachem, M.

To be published.

Macromolecule Content

Total Structure Weight: 53.77 kDa
Atom Count: 3,868
Modelled Residue Count: 474
Deposited Residue Count: 479
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-binding PCMH-type domain-containing protein	A	479	Phytophthora sojae	Mutation(s): 0 Gene Names: PHYSODRAFT_474098, PHYSODRAFT_476693
UniProt
Find proteins for G4YQ65 (Phytophthora sojae (strain P6497)) Explore G4YQ65 Go to UniProtKB: G4YQ65
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G4YQ65
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain B [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MAN (Subject of Investigation/LOI) Query on MAN Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
OXY (Subject of Investigation/LOI) Query on OXY Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]