2YD0
Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1 ERAP1
- PDB DOI: https://doi.org/10.2210/pdb2YD0/pdb
- Entry: 2YD0 supersedes: 2XDT
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2011-03-17 Released: 2011-04-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.215 
- R-Value Work: 0.152 
- R-Value Observed: 0.155 
This is version 2.0 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 |
ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 | 897 | Homo sapiens | Mutation(s): 0  EC: 3.4.11 Membrane Entity: Yes  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NZ08 (Homo sapiens) Explore Q9NZ08  Go to UniProtKB:  Q9NZ08 | |||||
PHAROS:  Q9NZ08 GTEx:  ENSG00000164307  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9NZ08 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BES Query on BES | I [auth A] | 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID C16 H24 N2 O4 VGGGPCQERPFHOB-RDBSUJKOSA-N | |||
NAG Query on NAG | D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
EDO Query on EDO | H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
K Query on K | F [auth A], G [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.215 
- R-Value Work: 0.152 
- R-Value Observed: 0.155 
- Space Group: P 6 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 200.948 | α = 90 |
b = 200.948 | β = 90 |
c = 114.222 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
SHARP | phasing |
Entry History 
Deposition Data
- Released Date: 2011-04-13  Deposition Author(s): Vollmar, M., Kochan, G., Krojer, T., Ugochukwu, E., Muniz, J.R.C., Raynor, J., Chaikuad, A., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S.
- This entry supersedes: 2XDT
Revision History (Full details and data files)
- Version 1.0: 2011-04-13
Type: Initial release - Version 1.1: 2012-10-03
Changes: Database references, Source and taxonomy, Version format compliance - Version 1.2: 2018-01-24
Changes: Database references - Version 1.3: 2019-03-27
Changes: Data collection, Derived calculations - Version 1.4: 2019-04-03
Changes: Data collection, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary