6XOK | pdb_00006xok

X-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb6XOK/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Thermomyces lanuginosus
Expression System: Aspergillus flavus
Mutation(s): No

Deposited: 2020-07-07 Released: 2020-10-14
Deposition Author(s): McPherson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.134 (Depositor), 0.139 (DCC)
R-Value Work:
0.104 (Depositor), 0.111 (DCC)
R-Value Observed:
0.106 (Depositor)

Starting Model: experimental
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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, S.B., Kalasky, A.

(2020) Current Enzyme Inhibition 16

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

Macromolecule Content

Total Structure Weight: 33.54 kDa
Atom Count: 2,733
Modeled Residue Count: 261
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate C₄₆ H₉₀ O₅ XHUXLZVWHLYNKB-SJARJILFSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.134 (Depositor), 0.139 (DCC)
R-Value Work: 0.104 (Depositor), 0.111 (DCC)
R-Value Observed: 0.106 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.373	α = 90
b = 76.373	β = 90
c = 241.551	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

McPherson, A.

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2023-10-18
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

6XOK | pdb_00006xok

X-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution

Literature

The crystal Structures of Thermomyces (Humicola) lanuginosa lipase in complex with enzymatic reactants

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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