5LDS

Structure of the porcine aminopeptidase N ectodomain

PDB DOI: https://doi.org/10.2210/pdb5LDS/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2016-06-27 Released: 2017-04-05
Deposition Author(s): Santiago, C., Reguera, J., Mudgal, G., Casasnovas, J.M.
Funding Organization(s): Spanish Ministry of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.169
R-Value Observed: 0.171

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: 440.53 kDa
Atom Count: 34,579
Modelled Residue Count: 3,595
Deposited Residue Count: 3,780
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A, B, C, D	945	Sus scrofa	Mutation(s): 0 Gene Names: ANPEP EC: 3.4.11.2
UniProt
Find proteins for P15145 (Sus scrofa) Explore P15145 Go to UniProtKB: P15145
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15145
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	6		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G67849DJ GlyCosmos: G67849DJ GlyGen: G67849DJ

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	F, G, H, I, J F, G, H, I, J, K, L, M, N, P, Q, R, S	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain R Focus chain S Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain R Focus chain S
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	4		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G31886NL GlyCosmos: G31886NL GlyGen: G31886NL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] FA [auth C] GA [auth C] AA [auth B], BA [auth B], CA [auth B], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], MA [auth D], NA [auth D], OA [auth D], PA [auth D], U [auth A], V [auth A], W [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain LA [auth D] SDF format, chain T [auth A] SDF format, chain Y [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth B]	EA [auth C], LA [auth D], T [auth A], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain LA [auth D] Focus chain T [auth A] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain LA [auth D] Focus chain T [auth A] Focus chain Y [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain KA [auth C] SDF format, chain QA [auth D] SDF format, chain X [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain X [auth A]	DA [auth B], KA [auth C], QA [auth D], X [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain KA [auth C] Focus chain QA [auth D] Focus chain X [auth A] Interactions & Density Focus chain DA [auth B] Focus chain KA [auth C] Focus chain QA [auth D] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.169
R-Value Observed: 0.171
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.67	α = 99.66
b = 78.77	β = 92.62
c = 223.87	γ = 111.33

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Science	Spain	BFU2011-23940, BIO2014-52683-R

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2017-04-19
Changes: Database references
Version 1.2: 2018-06-13
Changes: Data collection
Version 1.3: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary