1Y43 | pdb_00001y43

crystal structure of aspergilloglutamic peptidase from Aspergillus niger

PDB DOI: https://doi.org/10.2210/pdb1Y43/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger var. macrosporus
Mutation(s): No

Deposited: 2004-11-30 Released: 2005-12-13
Deposition Author(s): Sasaki, H., Nakagawa, A., Iwata, S., Muramatsu, T., Suganuma, M., Sawano, Y., Kojima, M., Kubota, K., Takahashi, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.226 (Depositor)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger

Sasaki, H., Nakagawa, A., Muramatsu, T., Suganuma, M., Sawano, Y., Kojima, M., Kubota, K., Takahashi, K., Tanokura, M.

(2004) Proc Jpn Acad Ser B Phys Biol Sci 80: 435-438

Macromolecule Content

Total Structure Weight: 22.77 kDa
Atom Count: 1,661
Modeled Residue Count: 203
Deposited Residue Count: 212
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspergillopepsin II light chain	A	39	Aspergillus niger var. macrosporus	Mutation(s): 0 EC: 3.4.23.19
UniProt
Find proteins for P24665 (Aspergillus niger) Explore P24665 Go to UniProtKB: P24665
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24665
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspergillopepsin II heavy chain	B	173	Aspergillus niger var. macrosporus	Mutation(s): 0 EC: 3.4.23.19
UniProt
Find proteins for P24665 (Aspergillus niger) Explore P24665 Go to UniProtKB: P24665
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24665
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.226 (Depositor)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.1	α = 90
b = 70.7	β = 90
c = 38.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MLPHARE	phasing
X-PLOR	refinement
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-12-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-12-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2013-02-27
Changes: Database references
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary