1R79 | pdb_00001r79

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta

PDB DOI: https://doi.org/10.2210/pdb1R79/pdb
BMRB: 10098

Classification: TRANSFERASE
Organism(s): Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2003-10-21 Released: 2004-04-21
Deposition Author(s): Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations, structures with the lowest energy, target function

wwPDB Validation 3D Report Full Report

Validation slider image for 1R79

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

Literature

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta

Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 8.96 kDa
Atom Count: 611
Modeled Residue Count: 84
Deposited Residue Count: 84
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacylglycerol kinase, delta	A	84	Homo sapiens	Mutation(s): 0 Gene Names: KAZUSA cDNA ha00914 EC: 2.7.1.107 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16760 (Homo sapiens) Explore Q16760 Go to UniProtKB: Q16760
PHAROS: Q16760 GTEx: ENSG00000077044
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations, structures with the lowest energy, target function

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-04-21

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2004-04-21
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2022-03-02
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-05-29
Changes: Data collection

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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.