6QXP

Protein peptide complex

PDB DOI: https://doi.org/10.2210/pdb6QXP/pdb

Classification: PLANT PROTEIN
Organism(s): Arabidopsis
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2019-03-07 Released: 2020-03-25
Deposition Author(s): Moussu, S., Caroline, C., Santos-Fernandez, G., Wehrle, S., Grossniklaus, U., Santiago, J.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.274
R-Value Work: 0.227
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 383.37 kDa
Atom Count: 24,293
Modelled Residue Count: 3,066
Deposited Residue Count: 3,336
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat extensin-like protein 2	A, B, C, D, E A, B, C, D, E, F, G, H	361	Arabidopsis	Mutation(s): 0 Gene Names: LRX2, At1g62440, F24O1.18, T3P18.1
UniProt
Find proteins for O48809 (Arabidopsis thaliana) Explore O48809 Go to UniProtKB: O48809
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O48809
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein RALF-like 4	I, J, K, L, M I, J, K, L, M, N, O, P	56	Arabidopsis	Mutation(s): 0 Gene Names: RALFL4, At1g28270, F3H9.8
UniProt
Find proteins for Q9FZA0 (Arabidopsis thaliana) Explore Q9FZA0 Go to UniProtKB: Q9FZA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FZA0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	AA [auth a], FA [auth f], Q, R, T, AA [auth a], FA [auth f], Q, R, T, V, X	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain FA [auth f] Focus chain Q Focus chain R Focus chain T Focus chain V Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain FA [auth f] Focus chain Q Focus chain R Focus chain T Focus chain V Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	S	4		N-Glycosylation	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], DA [auth d], EA [auth e], U, W, CA [auth c], DA [auth d], EA [auth e], U, W, Y	2		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain U Focus chain W Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain U Focus chain W Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	BA [auth b], Z	4		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain Z
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth E] SDF format, chain NA [auth E] SDF format, chain PA [auth F] SDF format, chain GA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth D] SDF format, chain MA [auth E] SDF format, chain OA [auth F] SDF format, chain QA [auth G] SDF format, chain RA [auth G] SDF format, chain SA [auth H] MOL2 format, chain HA [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain GA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain SA [auth H]	GA [auth A] HA [auth A] IA [auth A] JA [auth D] KA [auth D] GA [auth A], HA [auth A], IA [auth A], JA [auth D], KA [auth D], LA [auth E], MA [auth E], NA [auth E], OA [auth F], PA [auth F], QA [auth G], RA [auth G], SA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain SA [auth H] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain SA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.274
R-Value Work: 0.227
R-Value Observed: 0.230
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.988	α = 90
b = 119.988	β = 90
c = 305.736	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council	Switzerland	716358

Revision History (Full details and data files)

Version 1.0: 2020-03-25
Type: Initial release
Version 1.1: 2020-04-08
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

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Help and Resources

6QXP

Protein peptide complex

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)