PDB-9rwm: Crystal structure of human ADAMTS-5 Cb and Spacer domains

ID or keywords:

Entry

Database: PDB / ID: 9rwm

Title

Crystal structure of human ADAMTS-5 Cb and Spacer domains

Components

A disintegrin and metalloproteinase with thrombospondin motifs 5

Keywords

PROTEIN BINDING / spacer domain / jelly-roll / Cys rich domain

Function / homology

Function and homology information

Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / pulmonary valve morphogenesis / myoblast fusion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix binding / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / endocardial cushion morphogenesis / extracellular matrix disassembly ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.6 Å

Authors

Milani, M. / Mastrangelo, E.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Structure, substrate recognition and therapeutic targeting of the human ADAMTS-5 spacer domain.
Authors: Milani, M. / Visintin, M. / Krastanova, I. / Visentini, M. / Margotti, E. / Ugolini, G. / Bolognesi, M. / Rovati, L.C. / Mastrangelo, E.

History

Deposition	Jul 9, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 20, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9rwm.cif.gz	112.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9rwm.ent.gz	83.9 KB	Display	PDB format
PDBx/mmJSON format	9rwm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rw/9rwm ftp://data.pdbj.org/pub/pdb/validation_reports/rw/9rwm	HTTPS FTP

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Related structure data

Similar structure data	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	#28 - Apr 2002 Anthrax Toxin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (2) #44 - Aug 2003 Calmodulin similarity (1) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: A disintegrin and metalloproteinase with thrombospondin motifs 5

B: A disintegrin and metalloproteinase with thrombospondin motifs 5

C: A disintegrin and metalloproteinase with thrombospondin motifs 5

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	49.361, 78.270, 77.370
Angle α, β, γ (deg.)	90.000, 105.090, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	706 - 855
2	1	1	A	706 - 855
3	2	2	A	706 - 852
4	2	2	A	706 - 852
5	3	3	A	696 - 852
6	3	3	A	696 - 852

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	A disintegrin and metalloproteinase with thrombospondin motifs 5 / ADAM-TS 5 / ADAM-TS5 / ADAMTS-5 / A disintegrin and metalloproteinase with thrombospondin motifs 11 ...ADAM-TS 5 / ADAM-TS5 / ADAMTS-5 / A disintegrin and metalloproteinase with thrombospondin motifs 11 / ADAM-TS 11 / ADAMTS-11 / ADMP-2 / Aggrecanase-2 Mass: 21482.545 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS5, ADAMTS11, ADMP2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UNA0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.07 %
Crystal grow	Temperature: 293 K / Method: microbatch Details: 0.2 M Ammonium Acetate, 30% PEG 4000, 0.1 M Sodium citrate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8729 Å / Relative weight: 1
Reflection	Resolution: 2.6→36.14 Å / Num. obs: 17475 / % possible obs: 99.3 % / Redundancy: 2.76 % / CC_1/2: 0.984 / R_merge(I) obs: 0.153 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2.6→2.74 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2542 / CC_1/2: 0.374

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.6→34.69 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.902 / Cross valid method: FREE R-VALUE / ESU R: 1.055 / ESU R Free: 0.335
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2596	893	5.114 %
R_work	0.1925	16568	-
all	0.196	-	-
obs	-	17461	99.137 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 35.971 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.543 Å²	-0 Å²	-2.038 Å²
2-	-	0.819 Å²	-0 Å²
3-	-	-	-1.102 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→34.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3668	0	0	213	3881

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	3780
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3651
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.823	5096
X-RAY DIFFRACTION	r_angle_other_deg	0.807	1.785	8445
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.255	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.27	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.769	10	702
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.948	10	148
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	569
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4325
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	849
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	576
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.226	0.2	3171
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	1846
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	2050
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.194	0.2	187
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.029	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.193	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.273	0.2	103
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.265	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.351	3.594	1894
X-RAY DIFFRACTION	r_mcbond_other	3.349	3.594	1894
X-RAY DIFFRACTION	r_mcangle_it	5.406	6.443	2363
X-RAY DIFFRACTION	r_mcangle_other	5.405	6.443	2364
X-RAY DIFFRACTION	r_scbond_it	3.632	3.898	1886
X-RAY DIFFRACTION	r_scbond_other	3.631	3.899	1887
X-RAY DIFFRACTION	r_scangle_it	5.879	6.975	2728
X-RAY DIFFRACTION	r_scangle_other	5.878	6.975	2729
X-RAY DIFFRACTION	r_lrange_it	8.72	34.822	4082
X-RAY DIFFRACTION	r_lrange_other	8.712	34.619	4052
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.117	0.05	4475
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.105	0.05	4310
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.114	0.05	4502

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.1165	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.1165	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10514	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.10514	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11391	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11391	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.6-2.667	0.348	63	0.279	1210	0.283	1280	0.928	0.948	99.4531	0.279
2.667-2.74	0.366	75	0.277	1181	0.282	1262	0.919	0.951	99.5246	0.277
2.74-2.819	0.365	67	0.264	1120	0.269	1194	0.912	0.956	99.4137	0.264
2.819-2.905	0.359	58	0.256	1140	0.26	1206	0.928	0.958	99.3366	0.256
2.905-2.999	0.362	61	0.226	1078	0.233	1142	0.925	0.968	99.7373	0.226
2.999-3.104	0.327	58	0.236	1066	0.24	1132	0.937	0.964	99.2933	0.236
3.104-3.22	0.307	50	0.197	1009	0.202	1070	0.947	0.974	98.972	0.197
3.22-3.35	0.247	54	0.193	958	0.196	1026	0.96	0.977	98.6355	0.193
3.35-3.498	0.195	50	0.175	946	0.176	1003	0.976	0.982	99.3021	0.175
3.498-3.667	0.225	45	0.185	890	0.187	945	0.972	0.98	98.9418	0.185
3.667-3.862	0.237	47	0.182	860	0.185	914	0.967	0.981	99.2341	0.182
3.862-4.094	0.31	44	0.167	817	0.174	869	0.946	0.983	99.0794	0.167
4.094-4.372	0.192	39	0.156	747	0.158	792	0.983	0.986	99.2424	0.156
4.372-4.716	0.233	35	0.139	720	0.143	762	0.97	0.989	99.0814	0.139
4.716-5.156	0.199	34	0.138	666	0.141	707	0.973	0.988	99.0099	0.138
5.156-5.749	0.208	32	0.177	589	0.178	630	0.977	0.982	98.5714	0.177
5.749-6.609	0.297	27	0.191	528	0.195	560	0.96	0.981	99.1071	0.191
6.609-8.021	0.302	24	0.225	461	0.229	490	0.946	0.975	98.9796	0.225
8.021-11.052	0.125	19	0.16	357	0.158	380	0.987	0.985	98.9474	0.16
11.052-34.69	0.197	11	0.228	225	0.227	237	0.989	0.968	99.5781	0.228

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