4HX2

Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin

PDB DOI: https://doi.org/10.2210/pdb4HX2/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Bacillus licheniformis, Streptomyces caespitosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-09 Released: 2012-12-05
Deposition Author(s): Trillo-Muyo, S., Martinez-Rodriguez, S., Arolas, J.L., Gomis-Ruth, F.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.217
R-Value Work: 0.177
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes

Trillo-Muyo, S., Martinez-Rodriguez, S., Arolas, J.L., Gomis-Ruth, F.X.

(2013) Chem Sci 4: 791-797

DOI: https://doi.org/10.1039/C2SC21712K

Macromolecule Content

Total Structure Weight: 79.69 kDa
Atom Count: 5,900
Modelled Residue Count: 772
Deposited Residue Count: 776
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KerA	A, C	274	Bacillus licheniformis	Mutation(s): 0 EC: 3.4.21.62
UniProt
Find proteins for Q9FDF2 (Bacillus licheniformis) Explore Q9FDF2 Go to UniProtKB: Q9FDF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FDF2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutral proteinase inhibitor ScNPI	B, D	114	Streptomyces caespitosus	Mutation(s): 0 Gene Names: ScNPI
UniProt
Find proteins for Q9FDS0 (Streptomyces caespitosus) Explore Q9FDS0 Go to UniProtKB: Q9FDS0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FDS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1AX Query on 1AX Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	(2R,2'R)-3,3'-oxydipropane-1,2-diol C₆ H₁₄ O₅ GPLRAVKSCUXZTP-PHDIDXHHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth C] MOL2 format, chain K [auth A] MOL2 format, chain T [auth C]	K [auth A], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain T [auth C] Interactions & Density Focus chain K [auth A] Focus chain T [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B]	G [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain U [auth C] SDF format, chain V [auth D] MOL2 format, chain L [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth D]	L [auth A], U [auth C], V [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain U [auth C] Focus chain V [auth D] Interactions & Density Focus chain L [auth A] Focus chain U [auth C] Focus chain V [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C]	S [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C]	E [auth A], F [auth A], Q [auth C], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth C] Focus chain R [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	N [auth B], O [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.217
R-Value Work: 0.177
R-Value Observed: 0.177
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.969	α = 90
b = 83.624	β = 110.78
c = 77.617	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Trillo-Muyo, S.

Martinez-Rodriguez, S.

Arolas, J.L.

Gomis-Ruth, F.X.

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2013-02-20
Changes: Database references
Version 1.2: 2013-02-27
Changes: Database references
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description