4BKW | pdb_00004bkw

Crystal structure of the C-terminal region of human ZFYVE9

PDB DOI: https://doi.org/10.2210/pdb4BKW/pdb

Classification: RECEPTOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-04-30 Released: 2013-05-15
Deposition Author(s): Williams, E., Krojer, T., Vollmar, M., Shrestha, L., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.247 (Depositor), 0.258 (DCC)
R-Value Work:
0.203 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the C-Terminal Region of Human Zfyve9

Williams, E.

(2013) Ph D Thesis

Macromolecule Content

Total Structure Weight: 59.77 kDa
Atom Count: 3,781
Modeled Residue Count: 479
Deposited Residue Count: 531
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9	A	531	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O95405 (Homo sapiens) Explore O95405 Go to UniProtKB: O95405
PHAROS: O95405 GTEx: ENSG00000157077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-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 B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.247 (Depositor), 0.258 (DCC)
R-Value Work: 0.203 (Depositor), 0.205 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.751	α = 90
b = 113.751	β = 90
c = 155.098	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 1.1: 2017-09-13
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

4BKW | pdb_00004bkw

Crystal structure of the C-terminal region of human ZFYVE9

Literature

Crystal Structure of the C-Terminal Region of Human Zfyve9

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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