5MS3

Kallikrein-related peptidase 8 calcium complex

PDB DOI: https://doi.org/10.2210/pdb5MS3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-30 Released: 2018-01-17
Deposition Author(s): Debela, M., Magdolen, V., Skala, W., Bode, W., Brandstetter, H., Goettig, P.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.266
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Specificity profiles and antagonistic Ca2+ and Zn2+ regulation of human KLK8/neuropsin activity by modules identified in crystal structures

Debela, M., Magdolen, V., Skala, W., Craik, C.S., Schneider, E.L., Biniossek, M.L., Schilling, O., Elsaesser, B., Bode, W., Brandstetter, H., Goettig, P.

To be published.

Macromolecule Content

Total Structure Weight: 24.52 kDa
Atom Count: 1,796
Modelled Residue Count: 228
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallikrein-8	A	228	Homo sapiens	Mutation(s): 0 Gene Names: KLK8, NRPN, PRSS19, TADG14, UNQ283/PRO322 EC: 3.4.21.118
UniProt & NIH Common Fund Data Resources
Find proteins for O60259 (Homo sapiens) Explore O60259 Go to UniProtKB: O60259
PHAROS: O60259 GTEx: ENSG00000129455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60259
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.266
R-Value Work: 0.221
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.997	α = 90
b = 51.741	β = 90
c = 82.863	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P25003-B21

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description

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Deposit Data

Help and Resources

5MS3

Kallikrein-related peptidase 8 calcium complex

Specificity profiles and antagonistic Ca2+ and Zn2+ regulation of human KLK8/neuropsin activity by modules identified in crystal structures

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)