9DS0 | pdb_00009ds0

Crystal structure of sphA with MeVGQ

PDB DOI: https://doi.org/10.2210/pdb9DS0/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-26 Released: 2025-10-22
Deposition Author(s): Xi, W., Hai, Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.256 (Depositor), 0.255 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.207 (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

strucutre of PLP-dependent enzyme sphA with MeVGQ

Xi, W., Hai, Y., Chai, W., He, X.

To be published.

Macromolecule Content

Total Structure Weight: 216.69 kDa
Atom Count: 14,689
Modeled Residue Count: 1,846
Deposited Residue Count: 1,948
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A, B, C, D	487	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_3G14690 EC: 2.3.1.47 (PDB Primary Data), 2 (UniProt)
UniProt
Find proteins for Q4WYY5 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WYY5 Go to UniProtKB: Q4WYY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WYY5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BDC Query on A1BDC Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], K [auth C], O [auth D]	(2E,3E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pent-3-enoic acid C₁₃ H₁₇ N₂ O₇ P FKDLHLZQTNPLRB-ZMCOGPLKSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain O [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain H [auth B] MOL2 format, chain N [auth C] MOL2 format, chain H [auth B] mmCIF format, chain N [auth C] mmCIF format, chain H [auth B]	H [auth B], N [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Focus chain N [auth C] Interactions & Density Focus chain H [auth B] Focus chain N [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B]	J [auth B], L [auth C], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C]
ACY Query on ACY 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]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E]	R [auth E], S [auth E], T [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Interactions & Density Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth G] MOL2 format, chain Q [auth G] mmCIF format, chain Q [auth G]	Q [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth G] Interactions & Density Focus chain Q [auth G]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain P [auth F] MOL2 format, chain P [auth F] mmCIF format, chain P [auth F]	P [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth F] Interactions & Density Focus chain P [auth F]