9GKU

Crystal Structure of Propanil hydrolase (PrpH) from Sphingomonas sp. Y57

PDB DOI: https://doi.org/10.2210/pdb9GKU/pdb

Classification: HYDROLASE
Organism(s): Sphingomonas sp. Y57
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-26 Released: 2024-11-06
Deposition Author(s): Graf, L.G., Lammers, L., Palm, G.J., Schulze, S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.199
R-Value Work: 0.173
R-Value Observed: 0.174

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Distribution and diversity of classical deacylases in bacteria

Graf, L.G., Moreno-Yruela, C., Qin, C., Schulze, S., Palm, G.J., Schmoeker, O., Wang, N., Hocking, D., Jebeli, L., Girbardt, B., Berndt, L., Weis, D.M., Janetzky, M., Zuehlke, D., Sievers, S., Strugnell, R.A., Olsen, C.A., Hofmann, K., Lammers, M.

(2024) Nature Communications

Macromolecule Content

Total Structure Weight: 334.75 kDa
Atom Count: 25,009
Modelled Residue Count: 2,960
Deposited Residue Count: 3,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propanil hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	380	Sphingomonas sp. Y57	Mutation(s): 0 Gene Names: prpH
UniProt
Find proteins for G3JWV8 (Sphingomonas sp. Y57) Explore G3JWV8 Go to UniProtKB: G3JWV8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3JWV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth E]	AA [auth E] EA [auth F] IA [auth G] J [auth A] MA [auth H] AA [auth E], EA [auth F], IA [auth G], J [auth A], MA [auth H], N [auth B], R [auth C], S [auth C], Z [auth E]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain J [auth A] Focus chain MA [auth H] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain JA [auth G] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain NA [auth H] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain NA [auth H] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain NA [auth H]	BA [auth E] FA [auth F] JA [auth G] K [auth A] NA [auth H] BA [auth E], FA [auth F], JA [auth G], K [auth A], NA [auth H], O [auth B], T [auth C], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain NA [auth H] Focus chain O [auth B] Focus chain T [auth C] Focus chain W [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain LA [auth H] SDF format, chain M [auth B] SDF format, chain V [auth D] SDF format, chain Y [auth E] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain Q [auth C] MOL2 format, chain DA [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain DA [auth F] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth C]	DA [auth F] HA [auth G] I [auth A] LA [auth H] M [auth B] DA [auth F], HA [auth G], I [auth A], LA [auth H], M [auth B], Q [auth C], V [auth D], Y [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain LA [auth H] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Y [auth E]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain OA [auth H] SDF format, chain P [auth B] SDF format, chain X [auth D] SDF format, chain U [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain KA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C]	CA [auth E] GA [auth F] KA [auth G] L [auth A] OA [auth H] CA [auth E], GA [auth F], KA [auth G], L [auth A], OA [auth H], P [auth B], U [auth C], X [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain KA [auth G] Focus chain L [auth A] Focus chain OA [auth H] Focus chain P [auth B] Focus chain U [auth C] Focus chain X [auth D]