3UIM | pdb_00003uim

Structural basis for the impact of phosphorylation on plant receptor-like kinase BAK1 activation

PDB DOI: https://doi.org/10.2210/pdb3UIM/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-11-05 Released: 2012-05-23
Deposition Author(s): Lou, Z.Y., Yan, L.M., Ma, Y.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.277 (Depositor), 0.283 (DCC)
R-Value Work:
0.234 (Depositor), 0.241 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural basis for the impact of phosphorylation on the activation of plant receptor-like kinase BAK1

Yan, L., Ma, Y.Y., Liu, D., Wei, X., Sun, Y., Chen, X., Zhao, H., Zhou, J., Wang, Z., Shui, W., Lou, Z.Y.

(2012) Cell Res 22: 1304-1308

PubMed: 22547027 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2012.74
Primary Citation Related Structures:
3UIM

Macromolecule Content

Total Structure Weight: 38.02 kDa
Atom Count: 2,508
Modeled Residue Count: 297
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1	A	326	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BAK1 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q94F62 (Arabidopsis thaliana) Explore Q94F62 Go to UniProtKB: Q94F62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q94F62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.277 (Depositor), 0.283 (DCC)
R-Value Work: 0.234 (Depositor), 0.241 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.11	α = 90
b = 74.7	β = 93.72
c = 71.924	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2013-06-26
Changes: Database references
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.