6VTM | pdb_00006vtm

Human Cathepsin-G Inhibited by S. aureus EapH1

PDB DOI: https://doi.org/10.2210/pdb6VTM/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-02-13 Released: 2020-04-22
Deposition Author(s): 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: 1.60 Å
R-Value Free:
0.209 (Depositor), 0.214 (DCC)
R-Value Work:
0.174 (Depositor), 0.184 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Human Cathepsin-G Inhibited by S. aureus EapH1

Herdendorf, T.J., Rooijakkers, S.H.M., Geisbrecht, B.V.

(2020) J Biological Chem

Macromolecule Content

Total Structure Weight: 147.62 kDa
Atom Count: 11,227
Modeled Residue Count: 1,276
Deposited Residue Count: 1,292
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin G	A, C, D, G	224	Homo sapiens	Mutation(s): 0 EC: 3.4.21.20
UniProt & NIH Common Fund Data Resources
Find proteins for P08311 (Homo sapiens) Explore P08311 Go to UniProtKB: P08311
PHAROS: P08311 GTEx: ENSG00000100448
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08311
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP domain-containing protein	B, E, F, H	99	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: SAV2205
UniProt
Find proteins for A0A0H3K0M1 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3K0M1 Go to UniProtKB: A0A0H3K0M1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3K0M1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth G] SDF format, chain T [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain U [auth G] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain U [auth G] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth C] I [auth A], J [auth A], K [auth A], L [auth A], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth E], U [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.209 (Depositor), 0.214 (DCC)
R-Value Work: 0.174 (Depositor), 0.184 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.229	α = 113.58
b = 72.902	β = 91.17
c = 88.906	γ = 106.24

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

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	GM121511

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

6VTM | pdb_00006vtm

Human Cathepsin-G Inhibited by S. aureus EapH1

Literature

Crystal Structure of Human Cathepsin-G Inhibited by S. aureus EapH1

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt