9LFQ | pdb_00009lfq

Complex crystal structure of transaldolase AprG with GlcNAc from Streptoalloteichus tenebrarius

PDB DOI: https://doi.org/10.2210/pdb9LFQ/pdb

Classification: TRANSFERASE
Organism(s): Streptoalloteichus tenebrarius
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-08 Released: 2025-09-24
Deposition Author(s): Xie, Z.Z., Li, Q.R., Zhang, L.L., Huang, J.-W., He, Y.T., Chen, C.-C., Guo, R.-T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.230 (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

Apramycin Biosynthesis: Structure and Mechanism of Action of a New-Type Transaldolase AprG from Streptoalloteichus tenebrarius

Xie, Z., Zhang, L., Li, Q., Huang, J.W., He, Y., Zhang, H., Wang, X., Min, J., Chen, C.C., Guo, R.T.

(2025) ACS Catal : 16186-16196

DOI: https://doi.org/10.1021/acscatal.5c02753

Macromolecule Content

Total Structure Weight: 227.33 kDa
Atom Count: 16,121
Modeled Residue Count: 2,011
Deposited Residue Count: 2,070
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AprG	A, D, E	345	Streptoalloteichus tenebrarius	Mutation(s): 0 Gene Names: aprG
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AprG	B, C	345	Streptoalloteichus tenebrarius	Mutation(s): 0 Gene Names: aprG
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AprG	F	345	Streptoalloteichus tenebrarius	Mutation(s): 0 Gene Names: aprG
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
A1EJ0 (Subject of Investigation/LOI) Query on A1EJ0 Download Ideal Coordinates CCD File SDF format, chain T [auth E] MOL2 format, chain T [auth E] mmCIF format, chain T [auth E]	T [auth E]	N-Acetylglucosamine C₈ H₁₅ N O₆ MBLBDJOUHNCFQT-LXGUWJNJSA-N		Interactions Focus chain T [auth E] Interactions & Density Focus chain T [auth E]
A1EJ2 (Subject of Investigation/LOI) Query on A1EJ2 Download Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] O [auth C] P [auth C] Q [auth C] H [auth A], K [auth B], O [auth C], P [auth C], Q [auth C], U [auth E]	D-Erythrose C₄ H₈ O₄ YTBSYETUWUMLBZ-IUYQGCFVSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth E]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain S [auth D] SDF format, chain V [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth D] MOL2 format, chain V [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth D] mmCIF format, chain V [auth F]	I [auth A], J [auth A], M [auth B], S [auth D], V [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain S [auth D] Focus chain V [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain S [auth D] Focus chain V [auth F]
A1EJ3 (Subject of Investigation/LOI) Query on A1EJ3 Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain G [auth A]	G [auth A], N [auth C], R [auth D]	~{N}-(2-oxidanylideneethyl)ethanamide C₄ H₇ N O₂ KCRRYOSHXIMXSZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth C] Focus chain R [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1EJ4 Query on A1EJ4	B, C	L-PEPTIDE LINKING	C₁₀ H₁₉ N₃ O₃		LYS
A1EJ1 Query on A1EJ1	F	L-PEPTIDE LINKING	C₁₄ H₂₇ N₃ O₇		LYS