3RAJ

Crystal structure of human CD38 in complex with the Fab fragment of antibody HB7

• PDB DOI: https://doi.org/10.2210/pdb3RAJ/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Komagataella pastoris, Mus musculus
• Mutation(s): Yes 


• Deposited: 2011-03-28 Released: 2011-04-27 
• Deposition Author(s): Zhang, H., Lee, H.C., Hao, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.04 Å
• R-Value Free: 0.275 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Engineering a novel cytosolic form of CD38 for cyclic ADP-ribose dependent signaling

Zhang, H., Zhao, Y.J., Hao, Q., Lee, H.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.69 kDa 
• Atom Count: 5,034 
• Modelled Residue Count: 653 
• Deposited Residue Count: 688 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase 1	A	257	Homo sapiens	Mutation(s): 5  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of the Fab fragment of antibody HB7	B [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of the Fab fragment of antibody HB7	C [auth L]	211	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.04 Å
• R-Value Free: 0.275 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.664	α = 90
b = 271.521	β = 90
c = 136.661	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Zhang, H., Lee, H.C., Hao, Q.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary