4GLB

Structure of p-nitrobenzaldehyde inhibited lipase from Thermomyces lanuginosa at 2.69 A resolution

PDB DOI: https://doi.org/10.2210/pdb4GLB/pdb

Classification: HYDROLASE
Organism(s): Thermomyces lanuginosus
Mutation(s): No

Deposited: 2012-08-14 Released: 2012-09-05
Deposition Author(s): Kumar, M., Sinha, M., Mukherjee, J., Gupta, M.N., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.205
R-Value Work: 0.161
R-Value Observed: 0.164

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

Structure of p-nitrobenzaldehyde inhibited lipase from Thermomyces lanuginosa at 2.69 A resolution

Kumar, M., Sinha, M., Mukherjee, J., Gupta, M.N., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 59.17 kDa
Atom Count: 4,281
Modelled Residue Count: 538
Deposited Residue Count: 538
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	269	Thermomyces lanuginosus	Mutation(s): 0 EC: 3.1.1.3
UniProt
Find proteins for O59952 (Thermomyces lanuginosus) Explore O59952 Go to UniProtKB: O59952
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O59952
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XXH Query on XXH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	4-nitrobenzaldehyde C₇ H₅ N O₃ BXRFQSNOROATLV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.205
R-Value Work: 0.161
R-Value Observed: 0.164
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.911	α = 90
b = 139.911	β = 90
c = 80.448	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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Help and Resources

4GLB

Structure of p-nitrobenzaldehyde inhibited lipase from Thermomyces lanuginosa at 2.69 A resolution

Structure of p-nitrobenzaldehyde inhibited lipase from Thermomyces lanuginosa at 2.69 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)