2HL6

Structure of homologously expressed Ferrulate esterase of Aspergillus niger in complex with CAPS

PDB DOI: https://doi.org/10.2210/pdb2HL6/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2006-07-06 Released: 2006-10-31
Deposition Author(s): Parsiegla, G., Herpoel-Gimbert, I., Dubots, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.196
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 59.57 kDa
Atom Count: 4,856
Modelled Residue Count: 520
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Feruloyl esterase A	A, B	260	Aspergillus niger	Mutation(s): 0 Gene Names: faeA EC: 3.1.1.73
UniProt
Find proteins for O42807 (Aspergillus niger) Explore O42807 Go to UniProtKB: O42807
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O42807
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B]	I [auth A], R [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	G [auth A] H [auth A] L [auth B] M [auth B] N [auth B] G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.196
R-Value Work: 0.163
R-Value Observed: 0.165
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.52	α = 90
b = 51.7	β = 127.98
c = 99.588	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-10-31

Deposition Author(s):

Parsiegla, G.

Herpoel-Gimbert, I.

Dubots, J.

Revision History (Full details and data files)

Version 1.0: 2006-10-31
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

2HL6

Structure of homologously expressed Ferrulate esterase of Aspergillus niger in complex with CAPS

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources