5LPY | pdb_00005lpy

Crystal structure of the BRI1 kinase domain (865-1160) in complex with ATP from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb5LPY/pdb
Entry: 5LPY supersedes: 4OAB

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-08-15 Released: 2016-08-24
Deposition Author(s): Bojar, D., Martinez, J., Hothorn, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.248 (Depositor), 0.254 (DCC)
R-Value Work:
0.201 (Depositor), 0.212 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the BRI1 kinase domain (865-1160) in complex with ATP from Arabidopsis thaliana

Bojar, D., Martinez, J., Hothorn, M.

To be published.

Macromolecule Content

Total Structure Weight: 33.95 kDa
Atom Count: 2,225
Modeled Residue Count: 286
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BRASSINOSTEROID INSENSITIVE 1	A	296	Arabidopsis thaliana	Mutation(s): 1 Gene Names: BRI1, At4g39400, F23K16.30 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for O22476 (Arabidopsis thaliana) Explore O22476 Go to UniProtKB: O22476
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O22476
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-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: 2.30 Å
R-Value Free: 0.248 (Depositor), 0.254 (DCC)
R-Value Work: 0.201 (Depositor), 0.212 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.823	α = 90
b = 115.823	β = 90
c = 49.898	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-24

Deposition Author(s):

This entry supersedes: 4OAB

Revision History (Full details and data files)

Version 1.0: 2016-08-24
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
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.