2XQR

Crystal structure of plant cell wall invertase in complex with a specific protein inhibitor

PDB DOI: https://doi.org/10.2210/pdb2XQR/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Arabidopsis thaliana, Nicotiana tabacum
Expression System: Komagataella pastoris, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-09-07 Released: 2010-10-06
Deposition Author(s): Hothorn, M., Van den Ende, W., Lammens, W., Rybin, V., Scheffzek, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.210
R-Value Work: 0.183
R-Value Observed: 0.184

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: 475.51 kDa
Atom Count: 34,132
Modelled Residue Count: 4,098
Deposited Residue Count: 4,116
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1	A, C, E, G, I A, C, E, G, I, K	537	Arabidopsis thaliana	Mutation(s): 0 EC: 3.2.1.26
UniProt
Find proteins for Q43866 (Arabidopsis thaliana) Explore Q43866 Go to UniProtKB: Q43866
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q43866
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INVERTASE INHIBITOR	B, D, F, H, J B, D, F, H, J, L	149	Nicotiana tabacum	Mutation(s): 0
UniProt
Find proteins for O49908 (Nicotiana tabacum) Explore O49908 Go to UniProtKB: O49908
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O49908
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-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	M, O, Q, S, U M, O, Q, S, U, W	6		N-Glycosylation	Interactions Focus chain M Focus chain O Focus chain Q Focus chain S Focus chain U Focus chain W Interactions & Density Focus chain M Focus chain O Focus chain Q Focus chain S Focus chain U Focus chain W
Glycosylation Resources
GlyTouCan: G89333WS GlyCosmos: G89333WS GlyGen: G89333WS

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain GA [auth D] SDF format, chain KA [auth F] SDF format, chain OA [auth H] SDF format, chain SA [auth J] SDF format, chain WA [auth L] MOL2 format, chain BA [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain OA [auth H] MOL2 format, chain SA [auth J] MOL2 format, chain WA [auth L]	BA [auth B] GA [auth D] KA [auth F] OA [auth H] SA [auth J] BA [auth B], GA [auth D], KA [auth F], OA [auth H], SA [auth J], WA [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain GA [auth D] Focus chain KA [auth F] Focus chain OA [auth H] Focus chain SA [auth J] Focus chain WA [auth L] Interactions & Density Focus chain BA [auth B] Focus chain GA [auth D] Focus chain KA [auth F] Focus chain OA [auth H] Focus chain SA [auth J] Focus chain WA [auth L]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain FA [auth C] SDF format, chain JA [auth E] SDF format, chain NA [auth G] SDF format, chain RA [auth I] SDF format, chain VA [auth K] MOL2 format, chain AA [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain NA [auth G] MOL2 format, chain RA [auth I] MOL2 format, chain VA [auth K]	AA [auth A] FA [auth C] JA [auth E] NA [auth G] RA [auth I] AA [auth A], FA [auth C], JA [auth E], NA [auth G], RA [auth I], VA [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain FA [auth C] Focus chain JA [auth E] Focus chain NA [auth G] Focus chain RA [auth I] Focus chain VA [auth K] Interactions & Density Focus chain AA [auth A] Focus chain FA [auth C] Focus chain JA [auth E] Focus chain NA [auth G] Focus chain RA [auth I] Focus chain VA [auth K]
FRU Query on FRU Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain HA [auth E] SDF format, chain LA [auth G] SDF format, chain PA [auth I] SDF format, chain TA [auth K] SDF format, chain Y [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth G] MOL2 format, chain PA [auth I] MOL2 format, chain TA [auth K] MOL2 format, chain Y [auth A]	DA [auth C] HA [auth E] LA [auth G] PA [auth I] TA [auth K] DA [auth C], HA [auth E], LA [auth G], PA [auth I], TA [auth K], Y [auth A]	beta-D-fructofuranose C₆ H₁₂ O₆ RFSUNEUAIZKAJO-ARQDHWQXSA-N		Interactions Focus chain DA [auth C] Focus chain HA [auth E] Focus chain LA [auth G] Focus chain PA [auth I] Focus chain TA [auth K] Focus chain Y [auth A] Interactions & Density Focus chain DA [auth C] Focus chain HA [auth E] Focus chain LA [auth G] Focus chain PA [auth I] Focus chain TA [auth K] Focus chain Y [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain IA [auth E] SDF format, chain MA [auth G] SDF format, chain QA [auth I] SDF format, chain UA [auth K] SDF format, chain Z [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain IA [auth E] MOL2 format, chain MA [auth G] MOL2 format, chain QA [auth I] MOL2 format, chain UA [auth K] MOL2 format, chain Z [auth A]	CA [auth B] EA [auth C] IA [auth E] MA [auth G] QA [auth I] CA [auth B], EA [auth C], IA [auth E], MA [auth G], QA [auth I], UA [auth K], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain EA [auth C] Focus chain IA [auth E] Focus chain MA [auth G] Focus chain QA [auth I] Focus chain UA [auth K] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth C] Focus chain IA [auth E] Focus chain MA [auth G] Focus chain QA [auth I] Focus chain UA [auth K] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.210
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.98	α = 90
b = 199.98	β = 90
c = 111.16	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-10-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-06
Type: Initial release
Version 1.1: 2011-06-09
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-03-07
Changes: Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary

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2XQR

Crystal structure of plant cell wall invertase in complex with a specific protein inhibitor

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2