6SH2
Crystal structure of human neprilysin E584D in complex with C-type natriuretic peptide.
- PDB DOI: https://doi.org/10.2210/pdb6SH2/pdb
- Classification: PEPTIDE BINDING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Komagataella phaffii GS115
- Mutation(s): Yes
- Deposited: 2019-08-05 Released: 2019-09-25
- Funding Organization(s): Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.287
- R-Value Work: 0.243
This is version 1.3 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 |
| Neprilysin | A [auth AAA] | 696 | Homo sapiens | Mutation(s): 1 Gene Names: MME, EPN EC: 3.4.24.11 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P08473 (Homo sapiens) Explore P08473 Go to UniProtKB: P08473 | |||||
PHAROS: P08473 GTEx: ENSG00000196549 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P08473 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| C-type natriuretic peptide fragment (CNP) | B [auth DDD] | 4 | Homo sapiens | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| ZN Query on ZN | G [auth AAA] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | H [auth AAA], I [auth AAA] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.287
- R-Value Work: 0.243
- Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 109.267 | α = 90 |
| b = 109.267 | β = 90 |
| c = 112.579 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-09-25 Deposition Author(s): Moss, S., Subramanian, V., Acharya, K.R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | United Kingdom | 286 (AS-PhD2015b006) |
Revision History (Full details and data files)
- Version 1.0: 2019-09-25
Type: Initial release - Version 1.1: 2020-02-05
Changes: Data collection, Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
