6KD5

Deposited: 2019-06-30 Released: 2020-06-24
Deposition Author(s): Ohno, A., Maita, N., Okumura, Y., Nikawa, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 13	A	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 13	B	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 Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR	C	6	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

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

Unit Cell:

Software Package:

Entry History & Funding Information

Deposition Author(s):

Ohno, A.

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

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