5W7A

Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S262A mutant, with LPS (low quality saposin domain)

PDB DOI: https://doi.org/10.2210/pdb5W7A/pdb

Classification: HYDROLASE
Organism(s): Oryctolagus cuniculus
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2017-06-19 Released: 2018-01-03
Deposition Author(s): Gorelik, A., Illes, K., Nagar, B.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.262
R-Value Work: 0.240
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 65.39 kDa
Atom Count: 4,017
Modelled Residue Count: 485
Deposited Residue Count: 563
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyloxyacyl hydrolase small subunit	A	141	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: AOAH EC: 3.1.1.77 Membrane Entity: Yes
UniProt
Find proteins for O18823 (Oryctolagus cuniculus) Explore O18823 Go to UniProtKB: O18823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O18823
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyloxyacyl hydrolase large subunit	B	422	Oryctolagus cuniculus	Mutation(s): 1 Gene Names: AOAH EC: 3.1.1.77 Membrane Entity: Yes
UniProt
Find proteins for O18823 (Oryctolagus cuniculus) Explore O18823 Go to UniProtKB: O18823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O18823
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
FTT (Subject of Investigation/LOI) Query on FTT Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	3-HYDROXY-TETRADECANOIC ACID C₁₄ H₂₈ O₃ ATRNZOYKSNPPBF-CYBMUJFWSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	D [auth B], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.262
R-Value Work: 0.240
R-Value Observed: 0.241
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.578	α = 90
b = 123.199	β = 90
c = 125.918	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-03

Deposition Author(s):

Gorelik, A.

Illes, K.

Nagar, B.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-133535

Revision History (Full details and data files)

Version 1.0: 2018-01-03
Type: Initial release
Version 1.1: 2018-01-17
Changes: Database references
Version 1.2: 2018-01-31
Changes: Database references
Version 1.3: 2018-02-14
Changes: Database references
Version 1.4: 2020-01-08
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary