7ZKG | pdb_00007zkg

C-Methyltransferase PsmD from Streptomyces griseofuscus with bound cofactor (crystal form 2)

PDB DOI: https://doi.org/10.2210/pdb7ZKG/pdb

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

Deposited: 2022-04-13 Released: 2022-12-28
Deposition Author(s): Weiergraeber, O.H., Amariei, D.A., Pozhydaieva, N., Pietruszka, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.216 (Depositor), 0.187 (DCC)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD-Crystal Structure, Catalytic Mechanism, and Preparative Applications

Amariei, D.A., Pozhydaieva, N., David, B., Schneider, P., Classen, T., Gohlke, H., Weiergraber, O.H., Pietruszka, J.

(2022) ACS Catal

DOI: https://doi.org/10.1021/acscatal.2c04240

Macromolecule Content

Total Structure Weight: 63.37 kDa
Atom Count: 4,163
Modeled Residue Count: 504
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A, B	275	Streptomyces griseofuscus	Mutation(s): 0 Gene Names: psmD
UniProt
Find proteins for W8R3D8 (Streptomyces griseofuscus) Explore W8R3D8 Go to UniProtKB: W8R3D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8R3D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 J [auth A] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B]	J [auth A], N [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	H [auth A], I [auth A], L [auth B], M [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]