2NQA

Catalytic Domain of Human Calpain 8

PDB DOI: https://doi.org/10.2210/pdb2NQA/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Streptomyces roseus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-10-30 Released: 2006-11-14
Deposition Author(s): Davis, T.L., Paramanathan, R., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Structure of Human Calpain 8

Davis, T.L., Paramanathan, R., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 74.42 kDa
Atom Count: 5,413
Modelled Residue Count: 636
Deposited Residue Count: 660
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpain-8	A, B	326	Homo sapiens	Mutation(s): 0 Gene Names: CAPN8, NCL2 EC: 3.4.22.53
UniProt & NIH Common Fund Data Resources
Find proteins for P17655 (Homo sapiens) Go to UniProtKB: P17655
PHAROS: P17655 GTEx: ENSG00000162909
Find proteins for A6NHC0 (Homo sapiens) Explore A6NHC0 Go to UniProtKB: A6NHC0
PHAROS: A6NHC0 GTEx: ENSG00000203697
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6NHC0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leupeptin Inhibitor	C [auth D], D [auth E]	4	Streptomyces roseus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
AR7 Query on AR7	C [auth D], D [auth E]	PEPTIDE-LIKE	C₆ H₁₇ N₄ O₂		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000216 Query on PRD_000216	C [auth D], D [auth E]	LEUPEPTIN	Oligopeptide / Enzyme inhibitor		Interactions Focus chain C [auth D] Focus chain D [auth E] Interactions & Density Focus chain C [auth D] Focus chain D [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.268 (Depositor), 0.270 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.794	α = 90
b = 91.794	β = 90
c = 194.592	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-11-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-11-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2013-02-27
Changes: Other
Version 1.4: 2017-10-18
Changes: Advisory, Refinement description
Version 1.5: 2019-10-23
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.6: 2023-08-30
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.7: 2023-11-15
Changes: Data collection
Version 1.8: 2024-10-30
Changes: Structure summary