6SLR

Structure of saposin B in complex with atovaquone

PDB DOI: https://doi.org/10.2210/pdb6SLR/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-08-20 Released: 2020-09-09
Deposition Author(s): Zubieta, C., Milliken, B., Doyle, R.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.278
R-Value Work: 0.233
R-Value Observed: 0.235

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

Structure of saposin B in complex with atovaquone

Zubieta, C., Milliken, B., Doyle, R.

To be published.

Macromolecule Content

Total Structure Weight: 27.91 kDa
Atom Count: 1,997
Modelled Residue Count: 240
Deposited Residue Count: 243
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prosaposin	A, B, C	81	Homo sapiens	Mutation(s): 0 Gene Names: PSAP, GLBA, SAP1
UniProt & NIH Common Fund Data Resources
Find proteins for P07602 (Homo sapiens) Explore P07602 Go to UniProtKB: P07602
PHAROS: P07602 GTEx: ENSG00000197746
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07602
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AOQ (Subject of Investigation/LOI) Query on AOQ Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C]	F [auth B], G [auth C]	2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione C₂₂ H₁₉ Cl O₃ KUCQYCKVKVOKAY-CTYIDZIISA-N		Interactions Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain H [auth C]	D [auth B], E [auth B], H [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.278
R-Value Work: 0.233
R-Value Observed: 0.235
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.707	α = 90
b = 75.707	β = 90
c = 95.475	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Zubieta, C.

Milliken, B.

Doyle, R.

Funding Organization	Location	Grant Number
French National Research Agency	France	ATIP-Avenir

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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Help and Resources

6SLR

Structure of saposin B in complex with atovaquone

Structure of saposin B in complex with atovaquone

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)