6KEU | pdb_00006keu

Wildtype E53, a microbial HSL esterase

PDB DOI: https://doi.org/10.2210/pdb6KEU/pdb

Classification: HYDROLASE
Organism(s): Erythrobacter longus
Mutation(s): No

Deposited: 2019-07-05 Released: 2020-07-08
Deposition Author(s): Yang, X.C., Li, Z.Y., Xu, X.W., Li, J.X.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.179 (Depositor), 0.170 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Wildtype E53, a microbial HSL esterase

Yang, X.C., Yingyi, H., Li, Z.Y., Shuling, J., Zhen, R., Zhao, W., Henglin, C., Li, J.X., Xu, X.W.

To be published.

Macromolecule Content

Total Structure Weight: 134.1 kDa
Atom Count: 10,858
Modeled Residue Count: 1,236
Deposited Residue Count: 1,244
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B, C, D	311	Erythrobacter longus	Mutation(s): 0
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus) Explore A0A074MDU6 Go to UniProtKB: A0A074MDU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A074MDU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D8F (Subject of Investigation/LOI) Query on D8F Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain Y [auth D] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C]	E [auth A], J [auth B], S [auth C], Y [auth D]	(4-nitrophenyl) hexanoate C₁₂ H₁₅ N O₄ OLRXUEYZKCCEKK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain S [auth C] Focus chain Y [auth D]
6NA Query on 6NA Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Z [auth D]	AA [auth D] F [auth A] K [auth B] L [auth B] M [auth B] AA [auth D], F [auth A], K [auth B], L [auth B], M [auth B], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]