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

Starting Models: experimental
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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

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(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 E [auth A] SDF format, chain F [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [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

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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