5MJ6
Ligand-induced conformational change of Insulin-regulated aminopeptidase: insights on catalytic mechanism and active site plasticity.
- PDB DOI: https://doi.org/10.2210/pdb5MJ6/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2016-11-30 Released: 2017-04-05 
- Funding Organization(s): European Community's Seventh Framework Programme (FP7/2007-2013), Education and Lifelong Learning? of the National Strategic Reference Framework: Research Funding Program of the General Secretariat for Research & Technology, Harry J. Lloyd Charitable trust
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.53 Å
- R-Value Free: 0.229 
- R-Value Work: 0.174 
- R-Value Observed: 0.177 
This is version 2.1 of the entry. See complete history. 
Re-refinement Note
A newer entry is available that reflects an alternative modeling of the original data: 7ZYF
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Leucyl-cystinyl aminopeptidase | 881 | Homo sapiens | Mutation(s): 0  Gene Names: LNPEP, OTASE EC: 3.4.11.3 Membrane Entity: Yes  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UIQ6 (Homo sapiens) Explore Q9UIQ6  Go to UniProtKB:  Q9UIQ6 | |||||
PHAROS:  Q9UIQ6 GTEx:  ENSG00000113441  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9UIQ6 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-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 | C, R | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, F, K, N, P | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, H, J, L, M E, H, J, L, M, O, Q | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G, I | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
7O2 Query on 7O2 | X [auth A], XA [auth B] | [(2~{S})-2-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]-4,4-diphenyl-butyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid C35 H40 N3 O4 P FDAGDZVCWKCEEX-NGYIUDBNSA-N | |||
NAG Query on NAG | OA [auth B] PA [auth B] QA [auth B] RA [auth B] S [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BR Query on BR | AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] | BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M | |||
ZN Query on ZN | W [auth A], WA [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.53 Å
- R-Value Free: 0.229 
- R-Value Work: 0.174 
- R-Value Observed: 0.177 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 112.24 | α = 90 |
b = 143.17 | β = 90 |
c = 148.99 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-04-05  Deposition Author(s): Mpakali, A., Stratikos, E., Saridakis, E., Giastas, P.
Funding Organization | Location | Grant Number |
---|---|---|
European Community's Seventh Framework Programme (FP7/2007-2013) | United Kingdom | BioStruct-X (grant agreement No 283570) |
Education and Lifelong Learning? of the National Strategic Reference Framework: Research Funding Program of the General Secretariat for Research & Technology | Greece | grant no. ERC-14 to ES |
Harry J. Lloyd Charitable trust | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-04-05
Type: Initial release - Version 1.1: 2017-04-26
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary