9SM1 | pdb_00009sm1

FPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH and FPP

PDB DOI: https://doi.org/10.2210/pdb9SM1/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas chlororaphis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-05 Released: 2025-12-31
Deposition Author(s): Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.217 (Depositor), 0.222 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (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

Structural basis of methylation-triggered cyclization

Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 211.21 kDa
Atom Count: 15,000
Modeled Residue Count: 1,750
Deposited Residue Count: 1,788
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase domain protein	A, B, C, D, E A, B, C, D, E, F	298	Pseudomonas chlororaphis	Mutation(s): 0 Gene Names: PchlO6_6045
UniProt
Find proteins for A0AB33WVX4 (Pseudomonas chlororaphis O6) Explore A0AB33WVX4 Go to UniProtKB: A0AB33WVX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AB33WVX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 DA [auth D] SDF format, chain G [auth A] SDF format, chain IA [auth E] SDF format, chain KA [auth F] SDF format, chain V [auth C] SDF format, chain P [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B]	DA [auth D] G [auth A] IA [auth E] KA [auth F] P [auth B] DA [auth D], G [auth A], IA [auth E], KA [auth F], P [auth B], V [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain DA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain KA [auth F] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain KA [auth F] Focus chain P [auth B] Focus chain V [auth C]
FPP (Subject of Investigation/LOI) Query on FPP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain EA [auth D]	EA [auth D], H [auth A], Q [auth B], W [auth C]	FARNESYL DIPHOSPHATE C₁₅ H₂₈ O₇ P₂ VWFJDQUYCIWHTN-YFVJMOTDSA-N		Interactions Focus chain EA [auth D] Focus chain H [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain H [auth A] Focus chain Q [auth B] Focus chain W [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain MA [auth F] SDF format, chain J [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain MA [auth F] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain MA [auth F] mmCIF format, chain J [auth A]	AA [auth C] BA [auth C] CA [auth C] FA [auth D] GA [auth D] AA [auth C], BA [auth C], CA [auth C], FA [auth D], GA [auth D], HA [auth D], J [auth A], JA [auth E], K [auth A], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], O [auth A], R [auth B], S [auth B], T [auth B], U [auth B], X [auth C], Y [auth C], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]