6DWQ | pdb_00006dwq

Subtilisin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride

PDB DOI: https://doi.org/10.2210/pdb6DWQ/pdb

Classification: HYDROLASE
Organism(s): Bacillus licheniformis
Mutation(s): No

Deposited: 2018-06-27 Released: 2019-07-03
Deposition Author(s): Luo, M., Eaton, C.N., Phillips-Piro, C.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.148 (Depositor), 0.150 (DCC)
R-Value Work:
0.122 (Depositor), 0.120 (DCC)
R-Value Observed:
0.123 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Paired Spectroscopic and Crystallographic Studies of Protease Active Sites

Luo, M., Eaton, C.N., Hess, K.R., Phillips-Piro, C.M., Brewer, S.H., Fenlon, E.E.

(2019) ChemistrySelect 4: 9836-9843

Macromolecule Content

Total Structure Weight: 28.5 kDa
Atom Count: 2,473
Modeled Residue Count: 276
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KerA	A	274	Bacillus licheniformis	Mutation(s): 0 EC: 3.4.21.62
UniProt
Find proteins for P00780 (Bacillus licheniformis) Explore P00780 Go to UniProtKB: P00780
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00780
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A] D [auth A] E [auth A] G [auth A] H [auth A] B [auth A], D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], F [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	P [auth A], Q [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OSE Query on OSE	A	L-PEPTIDE LINKING	C₃ H₇ N O₆ S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.148 (Depositor), 0.150 (DCC)
R-Value Work: 0.122 (Depositor), 0.120 (DCC)
R-Value Observed: 0.123 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.926	α = 90
b = 67.926	β = 90
c = 123.481	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Luo, M.

Eaton, C.N.

Phillips-Piro, C.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R15GM093330

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2020-01-15
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description