5ARD

Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase

PDB DOI: https://doi.org/10.2210/pdb5ARD/pdb

Classification: HYDROLASE
Organism(s): Lederbergia lenta
Expression System: Bacillus subtilis
Mutation(s): Yes

Deposited: 2015-09-24 Released: 2016-09-14
Deposition Author(s): Sharma, M., Diaz-Rodriguez, A., Offen, W.A., Palm-Espling, M.E., Pordea, A., Wormald, M.R., Mcdonough, M., Davies, G.J., Davis, B.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.154
R-Value Work: 0.135
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cooperative Bio-Metallic Selectivity in a Tailored Protease Enables Creation of a C-C Cross-Coupling Heckase

Sharma, M., Diaz-Rodriguez, A., Offen, W.A., Palm-Espling, M.E., Pordea, A., Wormald, M.R., Mcdonough, M., Davies, G.J., Davis, B.G.

To be published.

Macromolecule Content

Total Structure Weight: 27.27 kDa
Atom Count: 2,211
Modelled Residue Count: 269
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBTILISIN SAVINASE	A	269	Lederbergia lenta	Mutation(s): 1 EC: 3.4.21.62
UniProt
Find proteins for P29600 (Lederbergia lenta) Explore P29600 Go to UniProtKB: P29600
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29600
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EI3 Query on EI3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	5-methyl-2-(5-methylpyridin-2-yl)pyridine C₁₂ H₁₂ N₂ PTRATZCAGVBFIQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.154
R-Value Work: 0.135
R-Value Observed: 0.136
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.059	α = 90
b = 61.28	β = 90
c = 74.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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5ARD

Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase

Cooperative Bio-Metallic Selectivity in a Tailored Protease Enables Creation of a C-C Cross-Coupling Heckase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)