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- PDB-2rjq: Crystal structure of ADAMTS5 with inhibitor bound -

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Basic information

Entry
Database: PDB / ID: 2rjq
TitleCrystal structure of ADAMTS5 with inhibitor bound
ComponentsADAMTS-5
KeywordsHYDROLASE / metalloprotease domain / aggrecanase / Cleavage on pair of basic residues / Extracellular matrix / Glycoprotein / Metal-binding / Secreted / Zymogen
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 ...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 / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / metallopeptidase activity / integrin binding / heparin binding / peptidase activity / collagen-containing extracellular matrix / endopeptidase activity / defense response to bacterium / endoplasmic reticulum lumen / proteolysis / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Peptidase M12B, ADAM-TS5 / YefM-like fold - #60 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain ...Peptidase M12B, ADAM-TS5 / YefM-like fold - #60 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / YefM-like fold / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BAT / A disintegrin and metalloproteinase with thrombospondin motifs 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMosyak, L. / Stahl, M. / Somers, W.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structures of the two major aggrecan degrading enzymes, ADAMTS4 and ADAMTS5.
Authors: Mosyak, L. / Georgiadis, K. / Shane, T. / Svenson, K. / Hebert, T. / McDonagh, T. / Mackie, S. / Olland, S. / Lin, L. / Zhong, X. / Kriz, R. / Reifenberg, E.L. / Collins-Racie, L.A. / ...Authors: Mosyak, L. / Georgiadis, K. / Shane, T. / Svenson, K. / Hebert, T. / McDonagh, T. / Mackie, S. / Olland, S. / Lin, L. / Zhong, X. / Kriz, R. / Reifenberg, E.L. / Collins-Racie, L.A. / Corcoran, C. / Freeman, B. / Zollner, R. / Marvell, T. / Vera, M. / Sum, P.E. / Lavallie, E.R. / Stahl, M. / Somers, W.
History
DepositionOct 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE THE CONSTRUCT THAT WAS CRYSTALLIZED ENCODES RESIDUES 262-628 OF HUMAN ADAMTS-5 PLUS A C- ... SEQUENCE THE CONSTRUCT THAT WAS CRYSTALLIZED ENCODES RESIDUES 262-628 OF HUMAN ADAMTS-5 PLUS A C-TERMINAL STREP-TAG (SEQUENCE: GSAWSHPQFEK).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAMTS-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8359
Polymers41,6511
Non-polymers1,1848
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.471, 95.471, 93.487
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ADAMTS-5 / / A disintegrin and metalloproteinase with thrombospondin motifs 5 / ADAM-TS 5 / ADAM-TS5 / ...A disintegrin and metalloproteinase with thrombospondin motifs 5 / ADAM-TS 5 / ADAM-TS5 / Aggrecanase-2 / ADMP-2 / ADAM-TS 11


Mass: 41651.238 Da / Num. of mol.: 1 / Fragment: Residues 262-628
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS5, ADAMTS11, ADMP2 / Cell line (production host): Ovary (CHO) cells / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q9UNA0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 88 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-BAT / 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE / BATIMASTAT / BB94 / Batimastat


Mass: 477.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H31N3O4S2 / Comment: inhibitor*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 8000, 0.2 M Ammonium sulfate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2006
RadiationMonochromator: Si 220, Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13624 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Rsym value: 0.29

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RJP

2rjp


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 22.759 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.533 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Although the amino acid sequence of the crystallized protein encompasses three domains: catalytic, disintegrin-like domain and ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Although the amino acid sequence of the crystallized protein encompasses three domains: catalytic, disintegrin-like domain and thrombospondin-like domain, the latter domain, residues 557-628, has no supporting electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 683 5 %RANDOM
Rwork0.23 ---
obs0.231 13609 87.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.82 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å21.93 Å20 Å2
2--3.85 Å20 Å2
3----5.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 66 81 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212349
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.9853186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8025291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60324.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73615394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0611513
X-RAY DIFFRACTIONr_chiral_restr0.0560.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021744
X-RAY DIFFRACTIONr_nbd_refined0.1670.2979
X-RAY DIFFRACTIONr_nbtor_refined0.290.21558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.283
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_mcbond_it0.1981.51486
X-RAY DIFFRACTIONr_mcangle_it0.3822321
X-RAY DIFFRACTIONr_scbond_it0.5493953
X-RAY DIFFRACTIONr_scangle_it1.0384.5865
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 18 -
Rwork0.339 434 -
all-452 -
obs--39.34 %
Refinement TLS params.

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

IDL11 (°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)
16.3094-1.3582-0.91235.34040.6916.37780.32930.33990.7812-0.1339-0.02-0.207-0.7394-0.2715-0.30930.06330.11160.114-0.26030.0398-0.1667-43.205-14.529915.0999
211.8705-1.4137-5.61263.14233.129111.0450.48950.27981.7469-0.45820.3132-0.7536-0.94280.6015-0.80280.1431-0.03310.11120.01780.00080.4197-19.1383-15.90998.0791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA264 - 4853 - 224
2X-RAY DIFFRACTION2AA486 - 555225 - 294

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