24UW | pdb_000024uw

Crystal structure of FPP-methyltransferase VbFPPMT from Variovorax boronicumulans PHE5-4 in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb24UW/pdb

Classification: TRANSFERASE
Organism(s): Variovorax boronicumulans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-03-22 Released: 2026-08-12
Deposition Author(s): Li, X.Q., Huang, J.-W., Chen, C.-C., Guo, R.-T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.233 (Depositor), 0.232 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (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

Crystal structure of FPP-methyltransferase VbFPPMT from Variovorax boronicumulans PHE5-4 in complex with SAH

Li, X.Q., Huang, J.-W., Chen, C.-C., Guo, R.-T.

To be published.

Macromolecule Content

Total Structure Weight: 214.11 kDa
Atom Count: 15,900
Modeled Residue Count: 1,743
Deposited Residue Count: 1,866
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FPP-methyltransferase VbFPPMT	A, B, C, D, E A, B, C, D, E, F	311	Variovorax boronicumulans	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F]	G [auth A] I [auth B] J [auth C] K [auth D] L [auth E] G [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F]
DTT Query on DTT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth F] MOL2 format, chain H [auth A] MOL2 format, chain N [auth F] mmCIF format, chain H [auth A] mmCIF format, chain N [auth F]	H [auth A], N [auth F]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain H [auth A] Focus chain N [auth F] Interactions & Density Focus chain H [auth A] Focus chain N [auth F]