5D67

Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb5D67/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-08-11 Released: 2015-09-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology, Partnership for Nuclear Receptor Signaling Code Biology (NHRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology

To be published.

Macromolecule Content

Total Structure Weight: 48.56 kDa
Atom Count: 3,319
Modelled Residue Count: 351
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EF-hand calcium-binding domain-containing protein 6	A, B, C, D	102	Homo sapiens	Mutation(s): 1 Gene Names: EFCAB6, DJBP, KIAA1672
UniProt & NIH Common Fund Data Resources
Find proteins for Q5THR3 (Homo sapiens) Explore Q5THR3 Go to UniProtKB: Q5THR3
PHAROS: Q5THR3 GTEx: ENSG00000186976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5THR3
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 E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D], R [auth D], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M35D67

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.407	α = 90
b = 67.187	β = 100.05
c = 70.697	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data scaling
XSCALE	data scaling
SHELX	phasing
SHARP	phasing
BUSTER	refinement
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Partnership for Nuclear Receptor Signaling Code Biology

Partnership for Nuclear Receptor Signaling Code Biology (NHRS)

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references

Prepare Data

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Deposit Data

Help and Resources

5D67

Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution

Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)