6AQ3 | pdb_00006aq3

Crystal structure of a trafficking protein particle complex subunit 3 from Naegleria fowleri covalently bound to palmitic acid

PDB DOI: https://doi.org/10.2210/pdb6AQ3/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Naegleria fowleri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-18 Released: 2017-08-30
Deposition Author(s): Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.209 (Depositor), 0.212 (DCC)
R-Value Work:
0.171 (Depositor), 0.176 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a trafficking protein particle complex subunit 3 from Naegleria fowleri covalently bound to palmitic acid

Edwards, T.E., Abendroth, J., Lorimer, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 136.79 kDa
Atom Count: 7,993
Modeled Residue Count: 1,014
Deposited Residue Count: 1,170
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
trafficking protein particle complex subunit 3	A, B, C, D, E A, B, C, D, E, F	195	Naegleria fowleri	Mutation(s): 0 Gene Names: NF0066220
UniProt
Find proteins for A0A2D0TCJ8 (Naegleria fowleri) Explore A0A2D0TCJ8 Go to UniProtKB: A0A2D0TCJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TCJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] N [auth C] P [auth D] R [auth E] G [auth A], J [auth B], N [auth C], P [auth D], R [auth E], V [auth F]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain W [auth F] SDF format, chain U [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain W [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain W [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] M [auth B] H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], O [auth C], Q [auth D], S [auth E], T [auth E], U [auth F], W [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.209 (Depositor), 0.212 (DCC)
R-Value Work: 0.171 (Depositor), 0.176 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.64	α = 114.55
b = 78.67	β = 87.67
c = 80.57	γ = 95.02

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Edwards, T.E.

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary