4DIR | pdb_00004dir

2.6 Angstrom X-ray structure of human CA(2+)-S100A5

PDB DOI: https://doi.org/10.2210/pdb4DIR/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-31 Released: 2013-02-13
Deposition Author(s): Liriano, M.A., Toth, E.A., Weber, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.283 (Depositor), 0.286 (DCC)
R-Value Work:
0.243 (Depositor), 0.234 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4DIR

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

Literature

Target-binding to S100A5 changes Ca(2+)-binding affinity and dynamics.

Liriano, M.A., Varney, K.M., Ishima, R., Toth, E.A., Weber, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 21.68 kDa
Atom Count: 1,201
Modeled Residue Count: 161
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A5	A, B	92	Homo sapiens	Mutation(s): 0 Gene Names: S100A5, S100D
UniProt & NIH Common Fund Data Resources
Find proteins for P33763 (Homo sapiens) Explore P33763 Go to UniProtKB: P33763
PHAROS: P33763 GTEx: ENSG00000196420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33763
Sequence Annotations Expand
Reference Sequence

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 C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.283 (Depositor), 0.286 (DCC)
R-Value Work: 0.243 (Depositor), 0.234 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.692	α = 90
b = 52.692	β = 90
c = 67.012	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.