6O9F | pdb_00006o9f

The structure of Thermomyces Lanuginosa lipase in complex with 1,3 diacylglycerol in a monoclinic crystal form

PDB DOI: https://doi.org/10.2210/pdb6O9F/pdb

Classification: HYDROLASE
Organism(s): Thermomyces lanuginosus
Expression System: Thermoactinomyces vulgaris
Mutation(s): No

Deposited: 2019-03-13 Released: 2024-05-01
Deposition Author(s): McPherson, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.214 (Depositor), 0.214 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants

McPherson , A., Larson , B.S., Kalasky , A.

(2020) Curr Enzym Inhib 16: 199-213

DOI: https://doi.org/10.2174/1573408016999200511090910

Macromolecule Content

Total Structure Weight: 198.35 kDa
Atom Count: 13,511
Modeled Residue Count: 1,614
Deposited Residue Count: 1,746
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 [auth E] E [auth D] A, B, C, D [auth E], E [auth D], F	291	Thermomyces lanuginosus	Mutation(s): 0 Gene Names: LIP EC: 3.1.1.3
UniProt
Find proteins for O59952 (Thermomyces lanuginosus) Explore O59952 Go to UniProtKB: O59952
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59952
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LTV (Subject of Investigation/LOI) Query on LTV Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain KA [auth F] SDF format, chain J [auth A] SDF format, chain FA [auth D] SDF format, chain AA [auth E] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth E] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth E]	AA [auth E] FA [auth D] J [auth A] KA [auth F] Q [auth B] AA [auth E], FA [auth D], J [auth A], KA [auth F], Q [auth B], W [auth C]	2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate C₄₆ H₉₀ O₅ XHUXLZVWHLYNKB-SJARJILFSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth D] Focus chain J [auth A] Focus chain KA [auth F] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth D] Focus chain J [auth A] Focus chain KA [auth F] Focus chain Q [auth B] Focus chain W [auth C]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain JA [auth F] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth E] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth E] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth E]	EA [auth D] I [auth A] JA [auth F] P [auth B] V [auth C] EA [auth D], I [auth A], JA [auth F], P [auth B], V [auth C], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth D] Focus chain I [auth A] Focus chain JA [auth F] Focus chain P [auth B] Focus chain V [auth C] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth D] Focus chain I [auth A] Focus chain JA [auth F] Focus chain P [auth B] Focus chain V [auth C] Focus chain Z [auth E]
OCA (Subject of Investigation/LOI) Query on OCA Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain S [auth C] SDF format, chain L [auth B] SDF format, chain HA [auth F] SDF format, chain G [auth A] SDF format, chain CA [auth D] MOL2 format, chain X [auth E] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B] MOL2 format, chain HA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth E] mmCIF format, chain S [auth C] mmCIF format, chain L [auth B] mmCIF format, chain HA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain CA [auth D]	CA [auth D] G [auth A] HA [auth F] L [auth B] S [auth C] CA [auth D], G [auth A], HA [auth F], L [auth B], S [auth C], X [auth E]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain G [auth A] Focus chain HA [auth F] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth E] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A] Focus chain HA [auth F] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth E]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain GA [auth D] SDF format, chain BA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain BA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain BA [auth E]	BA [auth E], GA [auth D], K [auth A], M [auth B], R [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth E] Focus chain GA [auth D] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth B] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth D] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain IA [auth F] SDF format, chain H [auth A] SDF format, chain DA [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain IA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain IA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth D]	DA [auth D] H [auth A] IA [auth F] N [auth B] O [auth B] DA [auth D], H [auth A], IA [auth F], N [auth B], O [auth B], T [auth C], U [auth C], Y [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth E] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth E]