8VIS

Human TMPRSS11D complexed with a disulfide-linked autoinhibitory DDDDK peptide

PDB DOI: https://doi.org/10.2210/pdb8VIS/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2024-01-05 Released: 2024-01-31
Deposition Author(s): Fraser, B.J., Dong, A., Ilyassov, O., Kenney, T., Li, Y.Y., Seitova, A., Li, Y., Hejazi, Z., Edwards, A., Benard, F., Arrowsmith, C.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.187 (Depositor), 0.200 (DCC)
R-Value Work:
0.155 (Depositor), 0.170 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of TMPRSS11D specificity and autocleavage activation

Fraser, B.J., Wilson, R.P., Ilyassov, O., Lac, J., Dong, A., Li, Y.Y., Seitova, A., Li, Y., Hejazi, Z., Kenney, T.M., Penn, L.Z., Edwards, A., Morin, G.B., Benard, F., Arrowsmith, C.H.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.10.09.617371

Macromolecule Content

Total Structure Weight: 173.48 kDa
Atom Count: 9,337
Modelled Residue Count: 1,015
Deposited Residue Count: 1,556
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 11D non-catalytic chain	A, C, E, G	145	Homo sapiens	Mutation(s): 5 Gene Names: TMPRSS11D, HAT EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for O60235 (Homo sapiens) Explore O60235 Go to UniProtKB: O60235
PHAROS: O60235 GTEx: ENSG00000153802
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60235
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 11D catalytic chain	B, D, F, H	244	Homo sapiens	Mutation(s): 0 Gene Names: TMPRSS11D, HAT EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for O60235 (Homo sapiens) Explore O60235 Go to UniProtKB: O60235
PHAROS: O60235 GTEx: ENSG00000153802
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60235
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth D] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D]	J [auth B], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth D] Interactions & Density Focus chain J [auth B] Focus chain L [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain S [auth H] MOL2 format, chain K [auth B] MOL2 format, chain S [auth H] mmCIF format, chain K [auth B] mmCIF format, chain S [auth H]	K [auth B], S [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain S [auth H] Interactions & Density Focus chain K [auth B] Focus chain S [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth E] SDF format, chain Q [auth H] MOL2 format, chain I [auth A] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth H] mmCIF format, chain I [auth A] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth H]	I [auth A], O [auth E], Q [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth E] Focus chain Q [auth H] Interactions & Density Focus chain I [auth A] Focus chain O [auth E] Focus chain Q [auth H]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain P [auth F] SDF format, chain R [auth H] SDF format, chain T [auth H] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain P [auth F] MOL2 format, chain R [auth H] MOL2 format, chain T [auth H] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain P [auth F] mmCIF format, chain R [auth H] mmCIF format, chain T [auth H]	M [auth D], N [auth D], P [auth F], R [auth H], T [auth H]	UNKNOWN ATOM OR ION X		Interactions Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth F] Focus chain R [auth H] Focus chain T [auth H] Interactions & Density Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth F] Focus chain R [auth H] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.187 (Depositor), 0.200 (DCC)
R-Value Work: 0.155 (Depositor), 0.170 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.676	α = 90
b = 119.676	β = 90
c = 134.289	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN154328
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM124165

Revision History (Full details and data files)

Version 1.0: 2024-01-31
Type: Initial release
Version 1.1: 2024-10-23
Changes: Database references, Structure summary

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Help and Resources

8VIS

Human TMPRSS11D complexed with a disulfide-linked autoinhibitory DDDDK peptide

Structural basis of TMPRSS11D specificity and autocleavage activation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2