5I85
aSMase with zinc and phosphocholine
- PDB DOI: https://doi.org/10.2210/pdb5I85/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2016-02-18 Released: 2016-09-07 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.222 
- R-Value Work: 0.190 
- R-Value Observed: 0.192 
This is version 2.2 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 |
Sphingomyelin phosphodiesterase | 583 | Homo sapiens | Mutation(s): 0  Gene Names: SMPD1, ASM EC: 3.1.4.12 Membrane Entity: Yes  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P17405 (Homo sapiens) Explore P17405  Go to UniProtKB:  P17405 | |||||
PHAROS:  P17405 GTEx:  ENSG00000166311  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P17405 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
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 | B | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 3 | |||||
---|---|---|---|---|---|
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 | C | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G10756ZZ GlyCosmos:  G10756ZZ GlyGen:  G10756ZZ |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A], F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PC Query on PC | U [auth A] | PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O | |||
SO4 Query on SO4 | J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ZN Query on ZN | H [auth A], I [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.222 
- R-Value Work: 0.190 
- R-Value Observed: 0.192 
- Space Group: P 64 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 131.601 | α = 90 |
b = 131.601 | β = 90 |
c = 188.573 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
CrystalClear | data collection |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
Entry History 
Deposition Data
- Released Date: 2016-09-07  Deposition Author(s): Zhou, Y.F., Wei, R.R.
Revision History (Full details and data files)
- Version 1.0: 2016-09-07
Type: Initial release - Version 1.1: 2016-11-16
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: 2021-03-24
Changes: Derived calculations, Source and taxonomy, Structure summary - Version 2.2: 2023-09-27
Changes: Data collection, Database references, Refinement description