2EF1 | pdb_00002ef1

Crystal structure of the extracellular domain of human CD38

PDB DOI: https://doi.org/10.2210/pdb2EF1/pdb
Entry: 2EF1 supersedes: 2DF1

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-02-20 Released: 2007-02-27
Deposition Author(s): Kukimoto-Niino, M., Nureki, O., Murayama, K., Shirouzu, M., Katada, T., Hara-Yokoyama, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.256 (Depositor), 0.255 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2EF1

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

Literature

Crystal structure of the extracellular domain of human CD38

Kukimoto-Niino, M., Nureki, O., Murayama, K., Shirouzu, M., Katada, T., Hara-Yokoyama, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 59.86 kDa
Atom Count: 4,185
Modeled Residue Count: 486
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase 1	A, B	256	Homo sapiens	Mutation(s): 0 Gene Names: CD38 EC: 3.2.2.5 (PDB Primary Data), 3.2.2 (UniProt), 3.2.2.6 (UniProt), 2.4.99.20 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens) Explore P28907 Go to UniProtKB: P28907
PHAROS: P28907 GTEx: ENSG00000004468
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28907
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.256 (Depositor), 0.255 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.593	α = 90
b = 51.164	β = 97.53
c = 101.135	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-02-27

Deposition Author(s):

Kukimoto-Niino, M.

Hara-Yokoyama, M.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

This entry supersedes: 2DF1

Revision History (Full details and data files)

Version 1.0: 2007-02-27
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: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary

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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.