5AVJ

Crystal structure of proteinase K from Engyodontium album

PDB DOI: https://doi.org/10.2210/pdb5AVJ/pdb

Classification: HYDROLASE
Organism(s): Parengyodontium album
Mutation(s): No

Deposited: 2015-06-17 Released: 2016-07-06
Deposition Author(s): Sugahara, M., Numata, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 ?
R-Value Free: 0.184
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

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

Literature

Derivatization of Proteinase K with Heavy Atoms Enhances Its Thermal Stability.

Yazawa, K., Sugahara, M., Yutani, K., Takehira, M., Numata, K.

(2016) ACS Catal 6: 3036-3046

DOI: https://doi.org/10.1021/acscatal.6b00100

Macromolecule Content

Total Structure Weight: 29.38 kDa
Atom Count: 2,427
Modelled Residue Count: 279
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 0 EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873 Go to UniProtKB: P06873
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06873
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 ?
R-Value Free: 0.184
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 67.549	α = 90
b = 67.549	β = 90
c = 107.083	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Sugahara, M.

Numata, K.

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

5AVJ

Crystal structure of proteinase K from Engyodontium album

Derivatization of Proteinase K with Heavy Atoms Enhances Its Thermal Stability.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)