1NHC

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger

PDB DOI: https://doi.org/10.2210/pdb1NHC/pdb

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

Deposited: 2002-12-19 Released: 2003-11-25
Deposition Author(s): van Pouderoyen, G., Snijder, H.J., Benen, J.A., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209
R-Value Work: 0.175
R-Value Observed: 0.176

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: 216.08 kDa
Atom Count: 16,429
Modelled Residue Count: 2,016
Deposited Residue Count: 2,016
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polygalacturonase I	A, B, C, D, E A, B, C, D, E, F	336	Aspergillus niger	Mutation(s): 0 EC: 3.2.1.15
UniProt
Find proteins for P26213 (Aspergillus niger) Explore P26213 Go to UniProtKB: P26213
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26213
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	6		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain OA [auth F] SDF format, chain V [auth C] SDF format, chain HA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain HA [auth E]	HA [auth E], OA [auth F], V [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth E] Focus chain OA [auth F] Focus chain V [auth C] Interactions & Density Focus chain HA [auth E] Focus chain OA [auth F] Focus chain V [auth C]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain K [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C]	AA [auth D] BA [auth D] FA [auth E] GA [auth E] J [auth A] AA [auth D], BA [auth D], FA [auth E], GA [auth E], J [auth A], K [auth A], NA [auth F], O [auth B], P [auth B], T [auth C], U [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain Y [auth C] SDF format, chain DA [auth D] SDF format, chain L [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C]	CA [auth D] DA [auth D] IA [auth E] JA [auth E] KA [auth E] CA [auth D], DA [auth D], IA [auth E], JA [auth E], KA [auth E], L [auth A], LA [auth E], M [auth A], PA [auth F], Q [auth B], QA [auth F], R [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain RA [auth F] SDF format, chain EA [auth D] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain S [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain EA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B]	EA [auth D], MA [auth E], N [auth A], RA [auth F], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain MA [auth E] Focus chain N [auth A] Focus chain RA [auth F] Focus chain S [auth B] Interactions & Density Focus chain EA [auth D] Focus chain MA [auth E] Focus chain N [auth A] Focus chain RA [auth F] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.012	α = 114.32
b = 84.13	β = 98
c = 96.035	γ = 89.75

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
EPMR	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-25
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary