8X78 | pdb_00008x78

Crystal Structure of N-Acyl Homoserine Lactone Lactonase from Pseudomonas poae

PDB DOI: https://doi.org/10.2210/pdb8X78/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas poae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-23 Released: 2025-02-26
Deposition Author(s): Li, X.H., Su, D.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.223 (Depositor), 0.225 (DCC)
R-Value Work:
0.168 (Depositor), 0.172 (DCC)
R-Value Observed:
0.169 (Depositor)

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

Crystal Structure of N-Acyl Homoserine Lactone Lactonase from Pseudomonas poae

Li, X.H., Su, D.

To be published.

Macromolecule Content

Total Structure Weight: 419.99 kDa
Atom Count: 28,197
Modeled Residue Count: 3,452
Deposited Residue Count: 3,672
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylase, beta-lactamase superfamily II	A [auth L] B [auth K] C [auth G] D [auth H] E [auth I] A [auth L], B [auth K], C [auth G], D [auth H], E [auth I], F [auth J], G [auth F], H [auth E], I [auth A], J [auth B], K [auth C], L [auth D]	306	Pseudomonas poae	Mutation(s): 0 Gene Names: SAMN04490208_1062
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Y [auth I] SDF format, chain X [auth H] SDF format, chain UA [auth D] SDF format, chain S [auth G] SDF format, chain RA [auth C] SDF format, chain P [auth K] SDF format, chain OA [auth B] SDF format, chain M [auth L] SDF format, chain LA [auth A] SDF format, chain IA [auth E] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain BA [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth H] MOL2 format, chain UA [auth D] MOL2 format, chain S [auth G] MOL2 format, chain RA [auth C] MOL2 format, chain P [auth K] MOL2 format, chain OA [auth B] MOL2 format, chain M [auth L] MOL2 format, chain LA [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain BA [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth H] mmCIF format, chain UA [auth D] mmCIF format, chain S [auth G] mmCIF format, chain RA [auth C] mmCIF format, chain P [auth K] mmCIF format, chain OA [auth B] mmCIF format, chain M [auth L] mmCIF format, chain LA [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain BA [auth J]	BA [auth J] EA [auth F] FA [auth F] IA [auth E] LA [auth A] BA [auth J], EA [auth F], FA [auth F], IA [auth E], LA [auth A], M [auth L], OA [auth B], P [auth K], RA [auth C], S [auth G], UA [auth D], X [auth H], Y [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth J] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth E] Focus chain LA [auth A] Focus chain M [auth L] Focus chain OA [auth B] Focus chain P [auth K] Focus chain RA [auth C] Focus chain S [auth G] Focus chain UA [auth D] Focus chain X [auth H] Focus chain Y [auth I] Interactions & Density Focus chain BA [auth J] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth E] Focus chain LA [auth A] Focus chain M [auth L] Focus chain OA [auth B] Focus chain P [auth K] Focus chain RA [auth C] Focus chain S [auth G] Focus chain UA [auth D] Focus chain X [auth H] Focus chain Y [auth I]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain WA [auth D] SDF format, chain W [auth H] SDF format, chain VA [auth D] SDF format, chain V [auth H] SDF format, chain U [auth G] SDF format, chain TA [auth C] SDF format, chain T [auth G] SDF format, chain SA [auth C] SDF format, chain R [auth K] SDF format, chain QA [auth B] SDF format, chain Q [auth K] SDF format, chain PA [auth B] SDF format, chain O [auth L] SDF format, chain NA [auth A] SDF format, chain N [auth L] SDF format, chain MA [auth A] SDF format, chain KA [auth E] SDF format, chain JA [auth E] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain DA [auth J] SDF format, chain CA [auth J] SDF format, chain AA [auth I] MOL2 format, chain Z [auth I] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth H] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth H] MOL2 format, chain U [auth G] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth G] MOL2 format, chain SA [auth C] MOL2 format, chain R [auth K] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth K] MOL2 format, chain PA [auth B] MOL2 format, chain O [auth L] MOL2 format, chain NA [auth A] MOL2 format, chain N [auth L] MOL2 format, chain MA [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth I] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth H] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth H] mmCIF format, chain U [auth G] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth G] mmCIF format, chain SA [auth C] mmCIF format, chain R [auth K] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth K] mmCIF format, chain PA [auth B] mmCIF format, chain O [auth L] mmCIF format, chain NA [auth A] mmCIF format, chain N [auth L] mmCIF format, chain MA [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth J] DA [auth J] GA [auth F] HA [auth F] AA [auth I], CA [auth J], DA [auth J], GA [auth F], HA [auth F], JA [auth E], KA [auth E], MA [auth A], N [auth L], NA [auth A], O [auth L], PA [auth B], Q [auth K], QA [auth B], R [auth K], SA [auth C], T [auth G], TA [auth C], U [auth G], V [auth H], VA [auth D], W [auth H], WA [auth D], Z [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth A] Focus chain N [auth L] Focus chain NA [auth A] Focus chain O [auth L] Focus chain PA [auth B] Focus chain Q [auth K] Focus chain QA [auth B] Focus chain R [auth K] Focus chain SA [auth C] Focus chain T [auth G] Focus chain TA [auth C] Focus chain U [auth G] Focus chain V [auth H] Focus chain VA [auth D] Focus chain W [auth H] Focus chain WA [auth D] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth A] Focus chain N [auth L] Focus chain NA [auth A] Focus chain O [auth L] Focus chain PA [auth B] Focus chain Q [auth K] Focus chain QA [auth B] Focus chain R [auth K] Focus chain SA [auth C] Focus chain T [auth G] Focus chain TA [auth C] Focus chain U [auth G] Focus chain V [auth H] Focus chain VA [auth D] Focus chain W [auth H] Focus chain WA [auth D] Focus chain Z [auth I]