Macromolecule Content

Total Structure Weight: 109.17 kDa
Atom Count: 8185
Modelled Residue Count: 972
Deposited Residue Count: 974
Unique protein chains: 1

3NV9

Crystal structure of Entamoeba histolytica Malic Enzyme

PDB DOI: 10.2210/pdb3NV9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-08 Released: 2011-07-20
Deposition Author(s): Dutta, D., Chakrabarty, A., Ghosh, S.K., Das, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.245
R-Value Work: 0.179
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

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

Literature

Structural and functional characterization of Entamoeba histolytica Malic enzyme

Chakrabarty, A., Dutta, D., Das, A.K., Ghosh, S.K.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malic enzyme	A, B	487	Entamoeba histolytica	Mutation(s): 0 Gene Names: EHI_044970, EhME EC: 1.1.1.40
UniProt
Find proteins for Q9NH04 (Entamoeba histolytica) Explore Q9NH04 Go to UniProtKB: Q9NH04
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NH04
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [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] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain C [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] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth B]	AA [auth B], DA [auth B], K [auth A], L [auth A], M [auth A], AA [auth B], DA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain O [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain O [auth A]	BA [auth B], CA [auth B], O [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Y [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Y [auth B]	J [auth A], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.245
R-Value Work: 0.179
R-Value Observed: 0.183
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.731	α = 90
b = 117.731	β = 90
c = 157.615	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
d*TREK	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2010-07-08
Released Date: 2011-07-20

Deposition Author(s):

Chakrabarty, A.

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.