9ATK

BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus

• PDB DOI: https://doi.org/10.2210/pdb9ATK/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-27 Released: 2024-06-12 
• Deposition Author(s): Mishra, N.B., Herdendorf, T.J., Geisbrecht, B.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.233 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Starting Models: experimental

Literature

Bifunctional Inhibition of Neutrophil Elastase and Cathepsin-G by Eap4 from S. aureus

Mishra, N.B., Geisbrecht, B.V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 250.34 kDa 
• Atom Count: 17,989 
• Modelled Residue Count: 2,156 
• Deposited Residue Count: 2,196 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil elastase	A, B [auth D], F [auth G], J	218	Homo sapiens	Mutation(s): 0  EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens) Explore P08246  Go to UniProtKB:  P08246
PHAROS:  P08246 GTEx:  ENSG00000197561
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P08246-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular Adherence Protein	C, E [auth F], H [auth I], L	108	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: map, SAV1938
UniProt
Find proteins for Q99QS1 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99QS1  Go to UniProtKB:  Q99QS1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin-G	D [auth E], G [auth H], I [auth B], K	223	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P08311 (Homo sapiens) Explore P08311  Go to UniProtKB:  P08311
PHAROS:  P08311 GTEx:  ENSG00000100448
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P08311-1

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	M, O, P, Q	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, R	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	S, T	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	U [auth E], V [auth H], W [auth B], X [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.233 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.207	α = 82.77
b = 85.527	β = 85.23
c = 89.536	γ = 83.6

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Mishra, N.B., Herdendorf, T.J., Geisbrecht, B.V.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM140852

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release