4CMH

Crystal structure of CD38 with a novel CD38-targeting antibody SAR650984

PDB DOI: https://doi.org/10.2210/pdb4CMH/pdb

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

Deposited: 2014-01-15 Released: 2014-07-16
Deposition Author(s): Deckert, J., Wetzel, M.C., Park, P.U., Bartle, L.M., Skaletskaya, A., Goldmacher, V., Vallee, F., ZhouLiu, Q., Ferrari, P., Pouzieux, S., Lahoute, C., Dumontet, C., Plesa, A., Chiron, M., Lejeune, P., Chittenden, T., Blanc, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.208
R-Value Work: 0.188
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

SAR650984, a novel humanized CD38-targeting antibody, demonstrates potent antitumor activity in models of multiple myeloma and other CD38+ hematologic malignancies.

Deckert, J., Wetzel, M.C., Bartle, L.M., Skaletskaya, A., Goldmacher, V.S., Vallee, F., Zhou-Liu, Q., Ferrari, P., Pouzieux, S., Lahoute, C., Dumontet, C., Plesa, A., Chiron, M., Lejeune, P., Chittenden, T., Park, P.U., Blanc, V.

(2014) Clin Cancer Res 20: 4574-4583

PubMed: 24987056 Search on PubMed
DOI: https://doi.org/10.1158/1078-0432.CCR-14-0695
Primary Citation of Related Structures:
4CMH

PubMed Abstract:
The CD38 cell surface antigen is expressed in diverse hematologic malignancies including multiple myeloma, B-cell non-Hodgkin lymphoma (NHL), B-cell chronic lymphocytic leukemia, B-cell acute lymphoblastic leukemia (ALL), and T-cell ALL. Here, we assessed the antitumor activity of the anti-CD38 antibody SAR650984.

Organizational Affiliation

Research and Development, ImmunoGen, Inc., Waltham, Massachusetts. jutta.deckert@immunogen.com.

Macromolecule Content

Total Structure Weight: 78.23 kDa
Atom Count: 5,901
Modelled Residue Count: 669
Deposited Residue Count: 704
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-RIBOSYL CYCLASE 1	A	256	Homo sapiens	Mutation(s): 4 EC: 3.2.2.5
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28907
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN OF SAR650984-FAB FRAGMENT	B	234	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF SAR650984-FAB FRAGMENT	C	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.208
R-Value Work: 0.188
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.619	α = 90
b = 111.492	β = 90
c = 147.877	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2014-09-10
Changes: Database references
Version 1.2: 2018-10-24
Changes: Data collection, Database references, Source and taxonomy, Structure summary