7A0K | pdb_00007a0k

Crystal structure of the entire ectodomain from the Physcomitrella patens receptor kinase CR4

PDB DOI: https://doi.org/10.2210/pdb7A0K/pdb

Classification: SIGNALING PROTEIN
Organism(s): Physcomitrium patens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2020-08-09 Released: 2021-08-18
Deposition Author(s): Hothorn, M., Okuda, S.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.216 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

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

Crystal structures of Arabidopsis and Physcomitrella CR4 reveal the molecular architecture of CRINKLY4 receptor kinases.

Okuda, S., Hothorn, L.A., Hothorn, M.

To be published.

Macromolecule Content

Total Structure Weight: 325.62 kDa
Atom Count: 21,072
Modeled Residue Count: 2,914
Deposited Residue Count: 3,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted protein	A, B, C, D, E A, B, C, D, E, F, G, H	383	Physcomitrium patens	Mutation(s): 0 Gene Names: PHYPA_009221, PHYPADRAFT_159650 EC: 2.7.11.1
UniProt
Find proteins for A9RKG8 (Physcomitrium patens) Explore A9RKG8 Go to UniProtKB: A9RKG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9RKG8
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, K, M, O, Q I, K, M, O, Q, S, T, U	2		N-Glycosylation	Interactions Focus chain I Focus chain K Focus chain M Focus chain O Focus chain Q Focus chain S Focus chain T Focus chain U Interactions & Density Focus chain I Focus chain K Focus chain M Focus chain O Focus chain Q Focus chain S Focus chain T Focus chain U
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain W [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain W [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain W [auth A]	CA [auth B] EA [auth C] GA [auth D] HA [auth E] IA [auth F] CA [auth B], EA [auth C], GA [auth D], HA [auth E], IA [auth F], JA [auth G], KA [auth G], MA [auth H], NA [auth H], W [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth B] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain W [auth A] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain W [auth A]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth C] SDF format, chain LA [auth G] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain LA [auth G] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain LA [auth G] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth B] BA [auth B] DA [auth B] FA [auth C] LA [auth G] AA [auth B], BA [auth B], DA [auth B], FA [auth C], LA [auth G], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain LA [auth G] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain LA [auth G] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]