6SBK | pdb_00006sbk

THERMOLYSIN IN COMPLEX WITH FRAGMENT J13

PDB DOI: https://doi.org/10.2210/pdb6SBK/pdb

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

Deposited: 2019-07-21 Released: 2020-08-26
Deposition Author(s): Magari, F., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.169 (Depositor), 0.171 (DCC)
R-Value Work:
0.150 (Depositor), 0.152 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

THERMOLYSIN IN COMPLEX WITH FRAGMENT J13

Magari, F., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.3 kDa
Atom Count: 2,794
Modeled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A [auth E]	316	Bacillus thermoproteolyticus	Mutation(s): 0 EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800 Go to UniProtKB: P00800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00800
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L4Z (Subject of Investigation/LOI) Query on L4Z Download:Ideal Coordinates CCD File SDF format, chain L [auth E] MOL2 format, chain L [auth E] mmCIF format, chain L [auth E]	L [auth E]	(2,5-dimethylpyrazol-3-yl)methylcarbamic acid C₇ H₁₁ N₃ O₂ GIQHHEQBVBVTAS-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Interactions & Density Focus chain L [auth E]
47J (Subject of Investigation/LOI) Query on 47J Download:Ideal Coordinates CCD File SDF format, chain K [auth E] MOL2 format, chain K [auth E] mmCIF format, chain K [auth E]	K [auth E]	1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine C₆ H₁₁ N₃ DAOWQCXPMWGSBW-UHFFFAOYSA-N		Interactions Focus chain K [auth E] Interactions & Density Focus chain K [auth E]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain J [auth E] MOL2 format, chain J [auth E] mmCIF format, chain J [auth E]	J [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth E] Interactions & Density Focus chain J [auth E]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain I [auth E] SDF format, chain G [auth E] MOL2 format, chain H [auth E] MOL2 format, chain I [auth E] MOL2 format, chain G [auth E] mmCIF format, chain H [auth E] mmCIF format, chain I [auth E] mmCIF format, chain G [auth E]	G [auth E], H [auth E], I [auth E]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Interactions & Density Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth E] MOL2 format, chain B [auth E] mmCIF format, chain B [auth E]	B [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth E] Interactions & Density Focus chain B [auth E]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain M [auth E] MOL2 format, chain M [auth E] mmCIF format, chain M [auth E]	M [auth E]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Interactions & Density Focus chain M [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth E] SDF format, chain F [auth E] SDF format, chain E SDF format, chain C [auth E] MOL2 format, chain D [auth E] MOL2 format, chain F [auth E] MOL2 format, chain E MOL2 format, chain C [auth E] mmCIF format, chain D [auth E] mmCIF format, chain F [auth E] mmCIF format, chain E mmCIF format, chain C [auth E]	C [auth E], D [auth E], E, F [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth E] Focus chain D [auth E] Focus chain E Focus chain F [auth E] Interactions & Density Focus chain C [auth E] Focus chain D [auth E] Focus chain E Focus chain F [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.169 (Depositor), 0.171 (DCC)
R-Value Work: 0.150 (Depositor), 0.152 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.561	α = 90
b = 92.561	β = 90
c = 129.273	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.