6KD5
Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor
- PDB DOI: https://doi.org/10.2210/pdb6KD5/pdb
- Classification: STRUCTURAL PROTEIN/INHIBITOR
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2019-06-30 Released: 2020-06-24 
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.236 
- R-Value Work: 0.184 
- R-Value Observed: 0.188 
wwPDB Validation   3D Report Full Report
This is version 3.2 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 |
Transmembrane protease serine 13 | 156 | Homo sapiens | Mutation(s): 0  Gene Names: TMPRSS13, MSP, TMPRSS11 EC: 3.4.21 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9BYE2 (Homo sapiens) Explore Q9BYE2  Go to UniProtKB:  Q9BYE2 | |||||
PHAROS:  Q9BYE2 GTEx:  ENSG00000137747  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9BYE2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Transmembrane protease serine 13 | 261 | Homo sapiens | Mutation(s): 1  Gene Names: TMPRSS13, MSP, TMPRSS11 EC: 3.4.21 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9BYE2 (Homo sapiens) Explore Q9BYE2  Go to UniProtKB:  Q9BYE2 | |||||
PHAROS:  Q9BYE2 GTEx:  ENSG00000137747  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9BYE2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR | 6 | synthetic construct | Mutation(s): 0  | ||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
CA Query on CA | I [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
AR7 Query on AR7 | C | PEPTIDE-LIKE | C6 H17 N4 O2 | ARG |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.236 
- R-Value Work: 0.184 
- R-Value Observed: 0.188 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 55.84 | α = 90 |
b = 62.4 | β = 90 |
c = 171.63 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-06-24  Deposition Author(s): Ohno, A., Maita, N., Okumura, Y., Nikawa, T.
Funding Organization | Location | Grant Number |
---|---|---|
Japan Society for the Promotion of Science (JSPS) | Japan | 15K13747 |
Japan Society for the Promotion of Science (JSPS) | Japan | 19K05696 |
Japan Society for the Promotion of Science (JSPS) | Japan | 15K09585 |
Japan Society for the Promotion of Science (JSPS) | Japan | 18K08453 |
Japan Society for the Promotion of Science (JSPS) | Japan | 15J40096 |
Japan Society for the Promotion of Science (JSPS) | Japan | 18H04981 |
Japan Society for the Promotion of Science (JSPS) | Japan | 19H04054 |
Japan Agency for Medical Research and Development (AMED) | Japan | JP19gm0810009 |
Revision History (Full details and data files)
- Version 1.0: 2020-06-24
Type: Initial release - Version 1.1: 2020-07-01
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.0: 2020-11-25
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary - Version 3.1: 2021-04-14
Changes: Database references - Version 3.2: 2023-11-22
Changes: Data collection, Database references, Refinement description