6WGZ | pdb_00006wgz

Crystal structure of HyBcl-2-4 with HyBak1 BH3

PDB DOI: https://doi.org/10.2210/pdb6WGZ/pdb

Classification: APOPTOSIS
Organism(s): Escherichia coli, Hydra vulgaris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-07 Released: 2021-04-21
Deposition Author(s): Kvansakul, M., Hinds, M.G., Banjara, S.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.251 (Depositor), 0.252 (DCC)
R-Value Work:
0.222 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structures of HyBcl-2-4 with HyBak1 BH3 and HyBax BH3

Banjara, S., Sa, J.D., Hinds, M.G., Kvansakul, M.

To be published.

Macromolecule Content

Total Structure Weight: 63.05 kDa
Atom Count: 4,384
Modeled Residue Count: 538
Deposited Residue Count: 559
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	A	371	Escherichia coli	Mutation(s): 0 Gene Names: DAH37_23060
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEX9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like 4	B	162	Hydra vulgaris	Mutation(s): 0 Gene Names: BCL2L1
UniProt
Find proteins for A7LM80 (Hydra vulgaris) Explore A7LM80 Go to UniProtKB: A7LM80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7LM80
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bak	C	26	Hydra vulgaris	Mutation(s): 0
UniProt
Find proteins for A1E3K5 (Hydra vulgaris) Explore A1E3K5 Go to UniProtKB: A1E3K5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1E3K5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	3		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009 Query on PRD_900009	D	alpha-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.251 (Depositor), 0.252 (DCC)
R-Value Work: 0.222 (Depositor), 0.223 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.245	α = 90
b = 73.65	β = 90
c = 140.8	γ = 90

Software Package:

Software Name	Purpose
xia2	data processing
PHASER	phasing
DIALS	data reduction
Aimless	data scaling
Coot	model building
PHENIX	refinement

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

Kvansakul, M.

Hinds, M.G.

Banjara, S.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP190103591

Revision History (Full details and data files)

Version 1.0: 2021-04-21
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary