7CIP | pdb_00007cip

Microbial Hormone-sensitive lipase E53 wild type

PDB DOI: https://doi.org/10.2210/pdb7CIP/pdb

Classification: HYDROLASE
Organism(s): Erythrobacter longus
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2020-07-08 Released: 2021-07-14
Deposition Author(s): Yang, X., Li, Z., Xu, X., Li, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.181 (Depositor), 0.181 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Microbial Hormone-sensitive lipase E53 wild type

Yang, X.

To be published.

Macromolecule Content

Total Structure Weight: 139.35 kDa
Atom Count: 11,012
Modeled Residue Count: 1,236
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B, C, D	314	Erythrobacter longus	Mutation(s): 0 Gene Names: EH31_02760
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus) Explore A0A074MDU6 Go to UniProtKB: A0A074MDU6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A074MDU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 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 UA [auth B] SDF format, chain T [auth A] SDF format, chain NC [auth D] SDF format, chain MB [auth C] MOL2 format, chain UA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain NC [auth D] MOL2 format, chain MB [auth C] mmCIF format, chain UA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain NC [auth D] mmCIF format, chain MB [auth C]	MB [auth C], NC [auth D], T [auth A], UA [auth B]	(4-nitrophenyl) hexanoate C₁₂ H₁₅ N O₄ OLRXUEYZKCCEKK-UHFFFAOYSA-N		Interactions Focus chain MB [auth C] Focus chain NC [auth D] Focus chain T [auth A] Focus chain UA [auth B] Interactions & Density Focus chain MB [auth C] Focus chain NC [auth D] Focus chain T [auth A] Focus chain UA [auth B]
NPO Query on NPO Download:Ideal Coordinates CCD File SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain LC [auth D] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain LC [auth D] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain LC [auth D]	LC [auth D], RA [auth B], SA [auth B]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain LC [auth D] Focus chain RA [auth B] Focus chain SA [auth B] Interactions & Density Focus chain LC [auth D] Focus chain RA [auth B] Focus chain SA [auth B]
6NA Query on 6NA Download:Ideal Coordinates CCD File SDF format, chain CC [auth D] SDF format, chain FB [auth C] SDF format, chain U [auth A] SDF format, chain IC [auth D] SDF format, chain G [auth A] MOL2 format, chain CC [auth D] MOL2 format, chain FB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain IC [auth D] MOL2 format, chain G [auth A] mmCIF format, chain CC [auth D] mmCIF format, chain FB [auth C] mmCIF format, chain U [auth A] mmCIF format, chain IC [auth D] mmCIF format, chain G [auth A]	CC [auth D], FB [auth C], G [auth A], IC [auth D], U [auth A]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain CC [auth D] Focus chain FB [auth C] Focus chain G [auth A] Focus chain IC [auth D] Focus chain U [auth A] Interactions & Density Focus chain CC [auth D] Focus chain FB [auth C] Focus chain G [auth A] Focus chain IC [auth D] Focus chain U [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A]	W [auth A], X [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain IB [auth C] SDF format, chain LB [auth C] SDF format, chain QA [auth B] SDF format, chain XA [auth C] SDF format, chain RB [auth D] SDF format, chain JB [auth C] SDF format, chain EB [auth C] SDF format, chain AC [auth D] MOL2 format, chain E [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain JB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain AC [auth D] mmCIF format, chain E [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain LB [auth C] mmCIF format, chain QA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain RB [auth D] mmCIF format, chain JB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain AC [auth D]	AC [auth D] E [auth A] EB [auth C] IB [auth C] JB [auth C] AC [auth D], E [auth A], EB [auth C], IB [auth C], JB [auth C], LB [auth C], QA [auth B], RB [auth D], XA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain E [auth A] Focus chain EB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain LB [auth C] Focus chain QA [auth B] Focus chain RB [auth D] Focus chain XA [auth C] Interactions & Density Focus chain AC [auth D] Focus chain E [auth A] Focus chain EB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain LB [auth C] Focus chain QA [auth B] Focus chain RB [auth D] Focus chain XA [auth C]
BUA Query on BUA Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain MA [auth B]	MA [auth B]	butanoic acid C₄ H₈ O₂ FERIUCNNQQJTOY-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Interactions & Density Focus chain MA [auth B]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain OB [auth C] SDF format, chain S [auth A] SDF format, chain ZB [auth D] SDF format, chain TA [auth B] SDF format, chain R [auth A] SDF format, chain PB [auth C] SDF format, chain OA [auth B] SDF format, chain NA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain DC [auth D] MOL2 format, chain OB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain TA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain DC [auth D] mmCIF format, chain OB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain ZB [auth D] mmCIF format, chain TA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain DC [auth D]	DC [auth D] IA [auth B] J [auth A] JA [auth B] K [auth A] DC [auth D], IA [auth B], J [auth A], JA [auth B], K [auth A], NA [auth B], OA [auth B], OB [auth C], PB [auth C], R [auth A], S [auth A], TA [auth B], ZB [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain DC [auth D] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PB [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth B] Focus chain ZB [auth D] Interactions & Density Focus chain DC [auth D] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PB [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth B] Focus chain ZB [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain H [auth A] SDF format, chain P [auth A] SDF format, chain SB [auth D] SDF format, chain WA [auth C] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] SDF format, chain Y [auth B] SDF format, chain WB [auth D] SDF format, chain VB [auth D] SDF format, chain VA [auth B] SDF format, chain UB [auth D] SDF format, chain NB [auth C] SDF format, chain MC [auth D] SDF format, chain KB [auth C] SDF format, chain I [auth A] SDF format, chain HB [auth C] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EC [auth D] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BB [auth C] SDF format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain P [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain WA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain WB [auth D] MOL2 format, chain VB [auth D] MOL2 format, chain VA [auth B] MOL2 format, chain UB [auth D] MOL2 format, chain NB [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain KB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EC [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain P [auth A] mmCIF format, chain SB [auth D] mmCIF format, chain WA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain WB [auth D] mmCIF format, chain VB [auth D] mmCIF format, chain VA [auth B] mmCIF format, chain UB [auth D] mmCIF format, chain NB [auth C] mmCIF format, chain MC [auth D] mmCIF format, chain KB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EC [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth C] BB [auth C] CA [auth B] DA [auth B] AA [auth B], AB [auth C], BB [auth C], CA [auth B], DA [auth B], EC [auth D], F [auth A], FA [auth B], H [auth A], HB [auth C], I [auth A], KB [auth C], MC [auth D], NB [auth C], P [auth A], SB [auth D], UB [auth D], VA [auth B], VB [auth D], WA [auth C], WB [auth D], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FA [auth B] Focus chain H [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain KB [auth C] Focus chain MC [auth D] Focus chain NB [auth C] Focus chain P [auth A] Focus chain SB [auth D] Focus chain UB [auth D] Focus chain VA [auth B] Focus chain VB [auth D] Focus chain WA [auth C] Focus chain WB [auth D] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FA [auth B] Focus chain H [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain KB [auth C] Focus chain MC [auth D] Focus chain NB [auth C] Focus chain P [auth A] Focus chain SB [auth D] Focus chain UB [auth D] Focus chain VA [auth B] Focus chain VB [auth D] Focus chain WA [auth C] Focus chain WB [auth D] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
CCN Query on CCN Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain O [auth A] SDF format, chain PA [auth B] SDF format, chain V [auth A] SDF format, chain YB [auth D] SDF format, chain XB [auth D] SDF format, chain TB [auth D] SDF format, chain Q [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KC [auth D] SDF format, chain JC [auth D] SDF format, chain HC [auth D] SDF format, chain HA [auth B] SDF format, chain GC [auth D] SDF format, chain GB [auth C] SDF format, chain GA [auth B] SDF format, chain FC [auth D] SDF format, chain EA [auth B] SDF format, chain DB [auth C] SDF format, chain CB [auth C] SDF format, chain BC [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain XB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KC [auth D] MOL2 format, chain JC [auth D] MOL2 format, chain HC [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain GC [auth D] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain FC [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain BC [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain YB [auth D] mmCIF format, chain XB [auth D] mmCIF format, chain TB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KC [auth D] mmCIF format, chain JC [auth D] mmCIF format, chain HC [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain GC [auth D] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain FC [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain BC [auth D]	BC [auth D] CB [auth C] DB [auth C] EA [auth B] FC [auth D] BC [auth D], CB [auth C], DB [auth C], EA [auth B], FC [auth D], GA [auth B], GB [auth C], GC [auth D], HA [auth B], HC [auth D], JC [auth D], KA [auth B], KC [auth D], L [auth A], LA [auth B], M [auth A], N [auth A], O [auth A], PA [auth B], Q [auth A], TB [auth D], V [auth A], XB [auth D], YB [auth D]	ACETONITRILE C₂ H₃ N WEVYAHXRMPXWCK-UHFFFAOYSA-N		Interactions Focus chain BC [auth D] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain FC [auth D] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain HA [auth B] Focus chain HC [auth D] Focus chain JC [auth D] Focus chain KA [auth B] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain TB [auth D] Focus chain V [auth A] Focus chain XB [auth D] Focus chain YB [auth D] Interactions & Density Focus chain BC [auth D] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain FC [auth D] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain HA [auth B] Focus chain HC [auth D] Focus chain JC [auth D] Focus chain KA [auth B] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain TB [auth D] Focus chain V [auth A] Focus chain XB [auth D] Focus chain YB [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain QB [auth C] MOL2 format, chain QB [auth C] mmCIF format, chain QB [auth C]	QB [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain QB [auth C] Interactions & Density Focus chain QB [auth C]