9GNF | pdb_00009gnf

A novel aminotransferase from Streptomyces sp. Gabaculine complex

PDB DOI: https://doi.org/10.2210/pdb9GNF/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp. BV333
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-02 Released: 2025-09-10
Deposition Author(s): De Rose, S.A., Isupov, M.N., Patti, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free:
0.185 (Depositor), 0.186 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)

Starting Model: experimental
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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

a novel aminotransferase from Streptomyces sp.

De Rose, S.A., Isupov, M.N., Patti, S.

To be published.

Macromolecule Content

Total Structure Weight: 104.57 kDa
Atom Count: 8,717
Modeled Residue Count: 909
Deposited Residue Count: 930
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptomyces aminotransferase	A, B	465	Streptomyces sp. BV333	Mutation(s): 0 EC: 2.6.1.1
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
PXG Query on PXG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID C₁₅ H₁₇ N₂ O₇ P WSOQXCGRIUHULI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B]	F [auth A], R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain R [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B]	D [auth A] E [auth A] G [auth A] H [auth A] I [auth A] D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], S [auth B], T [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	J [auth A], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]