7VMY | pdb_00007vmy

Crystal structure of LimF prenyltransferase bound with GSPP

PDB DOI: https://doi.org/10.2210/pdb7VMY/pdb

Classification: TRANSFERASE
Organism(s): Limnothrix sp. CACIAM 69d
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-09 Released: 2022-08-03
Deposition Author(s): Hamada, K., Kobayashi, S., Okada, C., Zhang, Y., Inoue, S., Goto, Y., Suga, H., Ogata, K., Sengoku, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates

Zhang, Y., Hamada, K., Nguyen, D.T., Inoue, S., Satake, M., Kobayashi, S., Okada, C., Ogata, K., Okada, M., Sengoku, T., Goto, Y., Suga, H.

(2022) Nat Catal

DOI: https://doi.org/10.1038/s41929-022-00822-2

Macromolecule Content

Total Structure Weight: 70.58 kDa
Atom Count: 5,228
Modeled Residue Count: 589
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LynF/TruF/PatF family peptide O-prenyltransferase	A, B	302	Limnothrix sp. CACIAM 69d	Mutation(s): 0 Gene Names: BJG00_018450
UniProt
Find proteins for A0ACD6BAH7 (Limnothrix sp. CACIAM 69d) Explore A0ACD6BAH7 Go to UniProtKB: A0ACD6BAH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GST (Subject of Investigation/LOI) Query on GST Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	GERANYL S-THIOLODIPHOSPHATE C₁₀ H₂₀ O₆ P₂ S AKIXWSDUEPPMKM-JXMROGBWSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
BTB (Subject of Investigation/LOI) Query on BTB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]