6BV1
Crystal structure of porcine aminopeptidase-N with Aspartic acid
- PDB DOI: https://doi.org/10.2210/pdb6BV1/pdb
- Classification: HYDROLASE
- Organism(s): Sus scrofa
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2017-12-12 Released: 2018-01-17 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.253 
- R-Value Work: 0.207 
- R-Value Observed: 0.210 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Aminopeptidase N | 902 | 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 AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B, C, F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | K [auth A], L [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ASP Query on ASP | M [auth A] | ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N | |||
SO4 Query on SO4 | N [auth A] O [auth A] P [auth A] Q [auth A] R [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ZN Query on ZN | X [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900017 Query on PRD_900017 | B, C, F | triacetyl-beta-chitotriose | Oligosaccharide / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.253 
- R-Value Work: 0.207 
- R-Value Observed: 0.210 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 259.81 | α = 90 |
b = 62.682 | β = 100.4 |
c = 81.717 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-01-17  Deposition Author(s): Chen, L., Lin, Y.-L., Li, F.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01AI089728 |
Revision History (Full details and data files)
- Version 1.0: 2018-01-17
Type: Initial release - Version 1.1: 2018-02-14
Changes: Author supporting evidence - Version 1.2: 2019-12-18
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary