6ODH | pdb_00006odh

BH3 domain swapped dimer of a BAK fragment

PDB DOI: https://doi.org/10.2210/pdb6ODH/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-26 Released: 2020-10-07
Deposition Author(s): Liu, L.-K.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.271 (Depositor), 0.276 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ODH

This is version 1.1 of the entry. See complete history.

Literature

A BAK fragment that binds mitochondrial lipids and releases cytochrome c

Dai, H., Liu, L.-K., Kaufmann, S.

To be published.

Macromolecule Content

Total Structure Weight: 59.94 kDa
Atom Count: 3,794
Modeled Residue Count: 452
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2 homologous antagonist/killer	A, B, C, D, E A, B, C, D, E, F	84	Homo sapiens	Mutation(s): 0 Gene Names: BAK1, BAK, BCL2L7, CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens) Explore Q16611 Go to UniProtKB: Q16611
PHAROS: Q16611 GTEx: ENSG00000030110
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16611
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain K [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], K [auth C], M [auth E], N [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain N [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain N [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain L [auth D] MOL2 format, chain O [auth F] MOL2 format, chain L [auth D] mmCIF format, chain O [auth F] mmCIF format, chain L [auth D]	L [auth D], O [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain O [auth F] Interactions & Density Focus chain L [auth D] Focus chain O [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.271 (Depositor), 0.276 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.043	α = 117.13
b = 55.039	β = 107.97
c = 55.682	γ = 97.55

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA166741

Revision History (Full details and data files)

Version 1.0: 2020-10-07
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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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.