3PNZ

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb3PNZ/pdb

Classification: HYDROLASE
Organism(s): Listeria monocytogenes serotype 4b str. H7858
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-20 Released: 2011-11-23
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes

Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 229.68 kDa
Atom Count: 17,578
Modelled Residue Count: 1,970
Deposited Residue Count: 1,980
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase family protein	A, B, C, D, E A, B, C, D, E, F	330	Listeria monocytogenes serotype 4b str. H7858	Mutation(s): 0 Gene Names: LMOh7858_2908
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
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain VA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] SDF format, chain WA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain WA [auth E]	DA [auth C] EA [auth C] FA [auth C] FB [auth F] GA [auth C] DA [auth C], EA [auth C], FA [auth C], FB [auth F], GA [auth C], GB [auth F], HB [auth F], K [auth A], L [auth A], M [auth A], MA [auth D], NA [auth D], OA [auth D], S [auth B], T [auth B], U [auth B], VA [auth E], WA [auth E], XA [auth E], YA [auth E], ZA [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] SDF format, chain HA [auth D] SDF format, chain Y [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain Y [auth C]	AA [auth C] AB [auth F] BB [auth F] CB [auth F] G [auth A] AA [auth C], AB [auth F], BB [auth F], CB [auth F], G [auth A], H [auth A], HA [auth D], IA [auth D], JA [auth D], N [auth B], O [auth B], P [auth B], PA [auth E], QA [auth E], RA [auth E], SA [auth E], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DB [auth F] SDF format, chain EB [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain R [auth B] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain Q [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain Q [auth B]	BA [auth C] CA [auth C] DB [auth F] EB [auth F] I [auth A] BA [auth C], CA [auth C], DB [auth F], EB [auth F], I [auth A], J [auth A], KA [auth D], LA [auth D], Q [auth B], R [auth B], TA [auth E], UA [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain UA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain UA [auth E]