5Y57 | pdb_00005y57

Crystal structure of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2

PDB DOI: https://doi.org/10.2210/pdb5Y57/pdb

Classification: HYDROLASE
Organism(s): Sphingobium faniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-07 Released: 2018-08-08
Deposition Author(s): Xu, D.Q., Ran, T.T., He, J., Wang, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.309 (Depositor), 0.310 (DCC)
R-Value Work:
0.255 (Depositor), 0.260 (DCC)
R-Value Observed:
0.258 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure and Catalytic Mechanism of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2

Xu, D.Q., Ran, T.T., He, J., Wang, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 190.24 kDa
Atom Count: 11,971
Modeled Residue Count: 1,512
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrethroid hydrolase	A, B, C, D, E A, B, C, D, E, F	288	Sphingobium faniae	Mutation(s): 0 Gene Names: pytH
UniProt
Find proteins for D0VUS3 (Sphingobium faniae) Explore D0VUS3 Go to UniProtKB: D0VUS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VUS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMS Query on PMS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	phenylmethanesulfonic acid C₇ H₈ O₃ S NIXKBAZVOQAHGC-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]