7WDW

DsyB in complex with SAH and MTHB

PDB DOI: https://doi.org/10.2210/pdb7WDW/pdb

Classification: TRANSFERASE
Organism(s): Nisaea denitrificans DSM 18348
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-22 Released: 2022-06-01
Deposition Author(s): Li, C.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.268
R-Value Work: 0.187
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB.

Li, C.Y., Crack, J.C., Newton-Payne, S., Murphy, A.R.J., Chen, X.L., Pinchbeck, B.J., Zhou, S., Williams, B.T., Peng, M., Zhang, X.H., Chen, Y.

(2022) mLife

DOI: https://doi.org/10.1002/mlf2.12030

Macromolecule Content

Total Structure Weight: 150.69 kDa
Atom Count: 10,644
Modelled Residue Count: 1,344
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DSYB	A, B, C, D	343	Nisaea denitrificans DSM 18348	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D]	E [auth A], G [auth B], J [auth C], M [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain M [auth D]
H9L (Subject of Investigation/LOI) Query on H9L Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D]	F [auth A], I [auth B], L [auth C], P [auth D]	4-methylsulfanyl-2-oxidanyl-butanoic acid C₅ H₁₀ O₃ S ONFOSYPQQXJWGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
TRS (Subject of Investigation/LOI) Query on TRS Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D]	H [auth B], K [auth C], N [auth D], O [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D]