9IVH | pdb_00009ivh

Structure of TF9 mutant of aminotransferase from Mycolicibacterium neoaurum in complex with LLP and G4O

PDB DOI: https://doi.org/10.2210/pdb9IVH/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium neoaurum VKM Ac-1815D
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-07-23 Released: 2025-07-30
Deposition Author(s): Wei, H., Cong, L., You, S., Liu, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: in silico
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Literature

Structure of TF9 mutant of aminotransferase from Mycolicibacterium neoaurum in complex with LLP and G4O

Wei, H., Cong, L., You, S., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 142.8 kDa
Atom Count: 10,650
Modeled Residue Count: 1,245
Deposited Residue Count: 1,292
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain amino acid transferase	A, B, C, D	323	Mycolicibacterium neoaurum VKM Ac-1815D	Mutation(s): 0 Gene Names: D174_04695 EC: 2.6.1.42
UniProt
Find proteins for A0A378TKC7 (Mycolicibacterium tokaiense) Explore A0A378TKC7 Go to UniProtKB: A0A378TKC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A378TKC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4O (Subject of Investigation/LOI) Query on G4O Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	propan-2-amine C₃ H₉ N JJWLVOIRVHMVIS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.615	α = 96.96
b = 78.586	β = 108.42
c = 91.541	γ = 113.07

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.