3VY7
Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-serine
- PDB DOI: https://doi.org/10.2210/pdb3VY7/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2012-09-21 Released: 2013-09-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.235 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
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 |
Zymogen granule membrane protein 16 | 141 | Homo sapiens | Mutation(s): 0  Gene Names: ZG16 Membrane Entity: Yes  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O60844 (Homo sapiens) Explore O60844  Go to UniProtKB:  O60844 | |||||
PHAROS:  O60844 GTEx:  ENSG00000174992  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O60844 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MAN Query on MAN | C [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N | |||
SER Query on SER | B [auth A] | SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N | |||
CL Query on CL | D [auth A], E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.235 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 58.8 | α = 90 |
b = 73 | β = 90 |
c = 30.3 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-09-25  Deposition Author(s): Kanagawa, M., Yamaguchi, Y.
Revision History (Full details and data files)
- Version 1.0: 2013-09-25
Type: Initial release - Version 1.1: 2014-09-03
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary