3VZG

Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine

PDB DOI: https://doi.org/10.2210/pdb3VZG/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-11 Released: 2013-10-16
Deposition Author(s): Kanagawa, M., Yamaguchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.288
R-Value Work: 0.217
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 15.87 kDa
Atom Count: 1,156
Modelled Residue Count: 138
Deposited Residue Count: 141
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zymogen granule membrane protein 16	A	141	Homo sapiens	Mutation(s): 0 Gene Names: ZG16
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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
THR Query on THR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.288
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.397	α = 90
b = 73.022	β = 90
c = 30.4	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-16

Deposition Author(s):

Kanagawa, M.

Yamaguchi, Y.

Revision History (Full details and data files)

Version 1.0: 2013-10-16
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

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Help and Resources

3VZG

Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)