8YVV | pdb_00008yvv

The Crystal Structure of BTK from Biortus

PDB DOI: https://doi.org/10.2210/pdb8YVV/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-03-29 Released: 2024-07-03
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Lin, D., Pan, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.266 (Depositor), 0.264 (DCC)
R-Value Work:
0.209 (Depositor), 0.214 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YVV

This is version 1.0 of the entry. See complete history.

Literature

The Crystal Structure of BTK from Biortus.

Wang, F., Cheng, W., Yuan, Z., Lin, D., Pan, W.

To be published.

Macromolecule Content

Total Structure Weight: 62.73 kDa
Atom Count: 4,429
Modeled Residue Count: 509
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A, B	266	Homo sapiens	Mutation(s): 0 Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187 Go to UniProtKB: Q06187
PHAROS: Q06187 GTEx: ENSG00000010671
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06187
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.266 (Depositor), 0.264 (DCC)
R-Value Work: 0.209 (Depositor), 0.214 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.686	α = 90
b = 102.995	β = 90
c = 117.543	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-03
Type: Initial release

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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.