PDB-7dha: crystal structure of CD38 in complex with daratumumab

ID or keywords:

Entry

Database: PDB / ID: 7dha

Title

crystal structure of CD38 in complex with daratumumab

Components

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Heavy Chain
Light chain

Keywords

IMMUNE SYSTEM / CD38 / antibody / daratumumab

Function / homology

Function and homology information

2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Lee, H.T. / Heo, Y.S.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of CD38 in complex with daratumumab, a first-in-class anti-CD38 antibody drug for treating multiple myeloma.
Authors: Lee, H.T. / Kim, Y. / Park, U.B. / Jeong, T.J. / Lee, S.H. / Heo, Y.S.

History

Deposition	Nov 13, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 22, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7dha.cif.gz	335.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7dha.ent.gz	228.5 KB	Display	PDB format
PDBx/mmJSON format	7dha.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7dha_validation.pdf.gz	452.7 KB	Display	wwPDB validaton report
Full document	7dha_full_validation.pdf.gz	461.9 KB	Display
Data in XML	7dha_validation.xml.gz	26.7 KB	Display
Data in CIF	7dha_validation.cif.gz	37.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/7dha ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dha	HTTPS FTP

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Related structure data

Related structure data	4cmhS S: Starting model for refinement
Similar structure data	4g80-1 4hkx-d 6cyf-3 4m5z-d 6vmj-3 7djz-d 7duo-d 4yk4-1 6cyf-2 7lcv-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1)

Deposited unit

A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1

B: Light chain

C: Heavy Chain

79.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	80.240, 54.160, 92.690
Angle α, β, γ (deg.)	90.000, 98.878, 90.000
Int Tables number	3
Space group name H-M	P121
Space group name Hall	P2y
Symmetry operation	#1: x,y,z #2: -x,y,-z

#1: Protein	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / 2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase 1 / ADPRC 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10 Mass: 30792.861 Da / Num. of mol.: 1 / Fragment: UNP residues 45-300 / Mutation: N56D, N120A, N175D, N209D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Antibody	Light chain Mass: 23405.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody	Heavy Chain Mass: 24931.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.09 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Lithium sulfate 0.1 M Bis-Tris 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.55→30 Å / Num. obs: 25496 / % possible obs: 98.05 % / Redundancy: 3.5 % / B_iso Wilson estimate: 42.99 Å² / CC_1/2: 0.998 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.55→2.61 Å / Num. unique obs: 2511 / CC_1/2: 0.843

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Processing

Software

Name	Version	Classification
MxDC		data collection
PHENIX	1.15.2_3472	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4CMH

4cmh

Resolution: 2.55→29.09 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7524

	R_factor	Num. reflection	% reflection
R_free	0.2614	2000	7.84 %
R_work	0.207	23496	-
obs	0.2112	25496	98.05 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 50.41 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→29.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5282	0	0	143	5425

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	5408
X-RAY DIFFRACTION	f_angle_d	0.7033	7348
X-RAY DIFFRACTION	f_chiral_restr	0.0448	819
X-RAY DIFFRACTION	f_plane_restr	0.0043	943
X-RAY DIFFRACTION	f_dihedral_angle_d	2.9897	3228

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.55-2.61	0.3232	140	0.2691	1649	X-RAY DIFFRACTION	97.65
2.61-2.68	0.3244	143	0.2704	1688	X-RAY DIFFRACTION	98.18
2.68-2.76	0.3558	139	0.265	1627	X-RAY DIFFRACTION	97.79
2.76-2.85	0.3587	143	0.2529	1671	X-RAY DIFFRACTION	98.16
2.85-2.95	0.316	140	0.2499	1650	X-RAY DIFFRACTION	98.14
2.95-3.07	0.3243	144	0.2463	1691	X-RAY DIFFRACTION	98.6
3.07-3.21	0.3367	144	0.2478	1694	X-RAY DIFFRACTION	98.5
3.21-3.38	0.2943	142	0.226	1664	X-RAY DIFFRACTION	98.21
3.38-3.59	0.264	142	0.2051	1671	X-RAY DIFFRACTION	98.05
3.59-3.87	0.2517	144	0.1876	1694	X-RAY DIFFRACTION	98.29
3.87-4.26	0.2293	142	0.1696	1659	X-RAY DIFFRACTION	98.2
4.26-4.87	0.1814	143	0.1554	1687	X-RAY DIFFRACTION	97.19
4.87-6.13	0.2263	144	0.1843	1688	X-RAY DIFFRACTION	97.55
6.13-29.09	0.2451	150	0.2114	1763	X-RAY DIFFRACTION	98.35

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.46033157623	-2.35324565718	0.586328040177	5.98125101648	2.14181670838	5.20722543817	0.135907426642	0.235091332624	0.15505320947	-0.0142946006865	-0.00743385074199	-0.167290900771	0.160246405033	0.355767841665	-0.120853717245	0.401997466158	-0.076207108461	-0.0743425465696	0.385294423635	0.138760284134	0.387317166379	12.2914445146	-28.8855173315	50.1025059896
2	5.02789227286	0.718817957631	-3.04763257624	4.673001983	0.894173694932	4.01758546083	-0.176905625162	-0.0892608618642	-0.636683235357	-0.346873965888	0.0351360334728	0.372399196244	0.374385651321	-0.282641018707	0.220836937762	0.571095351858	-0.196726489263	-0.088837743491	0.440444480647	0.179661395957	0.58413380954	16.2802924147	-14.8836924599	34.8366230259
3	3.39700800509	2.60460502003	-2.63393423119	3.65340992627	-2.31872524032	2.61836299852	-0.0999327794711	-0.0984978062232	0.111687170829	-0.00980002107358	-0.0564367561937	-0.00304217669301	-0.0424018470863	0.088959218543	0.0860681941861	0.366939533327	-0.0633923320637	-0.157542797114	0.339107223647	0.073173178875	0.373693038528	9.1284063826	-19.7028477116	46.2110614096
4	3.84676404867	0.55669523619	-0.084016608293	1.17265247989	1.15447611757	2.93079981585	-0.0322446346707	-0.0116840339918	0.00605864367504	-0.141592037605	0.0564207121214	0.308900755014	0.132981884991	-0.60987668724	-0.0231106757147	0.442915853383	-0.0581926743865	-0.0691792977417	0.355693425229	0.193454515532	0.504995841458	13.1857729852	-2.4867786834	33.1911494868
5	1.52502553112	-0.389762704158	-0.772066761554	3.69343729785	-1.17513953199	1.94206433868	-0.119831253889	0.115605367096	-0.129854648261	-0.803203996813	0.0783076016038	-0.265670077756	0.607357760345	0.19857306696	0.0154839408343	0.744811269964	0.0135053932367	0.0125382941977	0.259989678708	-0.0106875032529	0.456630831404	42.5135846322	-10.3955746458	19.2539543938
6	2.6182077187	1.68259354714	-2.29635345724	1.50800199271	-2.2499996819	3.11601819168	-0.236489465227	-0.0172453482247	-0.262576742467	-0.402367892946	-0.0775872085819	-0.192257082403	0.628593414061	0.400995929364	0.201839297841	0.531661403597	0.0406836947315	0.0574258725522	0.345188971804	-0.0664362479891	0.427060377284	51.5792065495	3.67739477965	12.4978768624
7	5.32474479326	1.06922974788	-1.94676631164	5.04256928247	-0.423391248911	4.29336712659	0.0258042141494	-0.360300416705	-0.230549759136	0.030971914911	-0.315025885992	-0.800090376225	0.492737229625	1.18120430848	0.263983830866	0.376116587408	0.110259665852	0.0374181012924	0.726558767275	0.0529308047998	0.391134264164	68.0123273539	14.9703619722	5.57554560243
8	5.44868389072	0.955764560588	2.19800782169	2.5177470199	-1.37500420259	2.92412106866	-0.427035400264	0.234503159725	0.330000728571	-0.430738124847	0.223881807032	0.114875159695	-0.279694107773	-0.136066434695	0.0157900014633	0.340488603173	0.0420722038251	0.0785329056502	0.21188199383	0.0653347924452	0.244054541951	35.5026124916	16.3769242867	21.8212822755
9	2.38337729138	0.560194154795	-0.0606344984305	2.40440846192	-0.366051518263	1.60319721648	-0.125298209008	0.025091340308	-0.0924596558599	-0.176749931954	0.225488651556	0.042123079327	0.0371801577247	-0.283127886656	-0.133383761007	0.406223476055	-0.046381366927	-0.00927076190472	0.240823993873	0.0574224569621	0.304059768756	31.1180511497	7.32977801702	25.1280003812
10	1.95820725449	0.352432234551	-0.238748702844	1.27399074926	-0.406280411122	0.480157510466	-0.0243409924284	-0.0816708980546	-0.183202702551	-0.140254665183	0.0981185308558	0.0293487987192	0.00756112143657	-0.135667042726	-0.0937173665475	0.395042878133	-0.0186593699618	-0.0149810749704	0.246218581433	0.000885961403092	0.297010997173	34.235914413	10.2567862347	27.1936728392
11	6.90695960988	1.88819082618	1.0410842222	2.81666449548	-0.585941651879	2.70364306294	0.639029556324	0.425618371701	0.123448903753	-0.936637998543	0.853799881019	-1.47273566144	0.858270589745	1.25279991573	-1.24924598349	0.744842774606	0.051148971897	0.0608858985124	0.879066930874	-0.0713327994506	0.503844965313	61.300049575	21.5903901066	-3.91685366073
12	3.22008406789	-1.68365138047	-3.61473370547	2.08652051514	1.30971629321	5.3285224622	-0.00949403797044	0.104061639134	-0.0454294443954	0.0645660232709	-0.121917051838	0.194269584422	0.257833922614	0.00793546450826	0.18723693269	0.286085684006	-0.0548756586119	-0.00131680582502	0.273479247873	0.000489234676471	0.287517585012	52.1372399831	19.1098273094	7.56985326289
13	0.449465262093	-0.0603644915156	-0.0449832158041	4.06350662601	2.3745404918	5.3646236463	0.0779869460635	0.294483119972	0.132600049272	-0.524011010455	-0.145798886417	0.25173833458	-0.524142950173	0.269801998546	0.183530178701	0.306960607431	-0.0401976458489	-0.0128596155206	0.405436862422	0.0237705577	0.333184969165	50.1749575189	22.7464897958	0.355551350259

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 94 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 95 through 165 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 166 through 257 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 75 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 76 through 128 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 129 through 212 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 17 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 18 through 57 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 58 through 128 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 129 through 143 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 144 through 184 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 185 through 222 )

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