8ZLF | pdb_00008zlf

Crystal structure of DH domain of FYVE Domain containing protein(FP10) from Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb8ZLF/pdb

Classification: SIGNALING PROTEIN
Organism(s): Entamoeba histolytica HM-1:IMSS-A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-19 Released: 2025-05-21
Deposition Author(s): Gautam, A.K., Umarao, P., Gourinath, S.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.289 (Depositor), 0.285 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

crystal structure of DH domain of FYVE domain containing Protein(FP10) from Entamoeba histolytica

Gautam, A.K., Umarao, P., Gourinath, S.

To be published.

Macromolecule Content

Total Structure Weight: 48.62 kDa
Atom Count: 3,128
Modeled Residue Count: 396
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho/RAC guanine nucleotide exchange factor, putative	A, B	209	Entamoeba histolytica HM-1:IMSS-A	Mutation(s): 0 Gene Names: EHI7A_047060
UniProt
Find proteins for N9UU15 (Entamoeba histolytica HM-1:IMSS-A) Explore N9UU15 Go to UniProtKB: N9UU15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	N9UU15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.289 (Depositor), 0.285 (DCC)
R-Value Work: 0.234 (Depositor), 0.235 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.59	α = 90
b = 69.337	β = 118.275
c = 57.615	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	--

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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.