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- PDB-2rjp: Crystal structure of ADAMTS4 with inhibitor bound -

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Basic information

Entry
Database: PDB / ID: 2rjp
TitleCrystal structure of ADAMTS4 with inhibitor bound
ComponentsADAMTS-4
KeywordsHYDROLASE / metalloprotease domain / aggrecanase / Cleavage on pair of basic residues / Extracellular matrix / Glycoprotein / Metal-binding / Polymorphism / Secreted / Zinc / Zymogen
Function / homology
Function and homology information


ADAMTS-4 endopeptidase / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / skeletal system development / metalloendopeptidase activity / metallopeptidase activity ...ADAMTS-4 endopeptidase / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / skeletal system development / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / collagen-containing extracellular matrix / protease binding / nuclear speck / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
YefM-like fold - #60 / 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 ...YefM-like fold - #60 / 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-886 / A disintegrin and metalloproteinase with thrombospondin motifs 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 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: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAMTS-4
B: ADAMTS-4
C: ADAMTS-4
D: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,66824
Polymers136,8874
Non-polymers2,78120
Water2,162120
1
A: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9176
Polymers34,2221
Non-polymers6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9176
Polymers34,2221
Non-polymers6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9176
Polymers34,2221
Non-polymers6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9176
Polymers34,2221
Non-polymers6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.566, 82.618, 99.326
Angle α, β, γ (deg.)90.000, 90.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPLYSAA227 - 22915 - 17
21ASPLYSBB227 - 22915 - 17
31ASPLYSCC227 - 22915 - 17
41ASPLYSDD227 - 22915 - 17
12THRCYSAA337 - 339125 - 127
22THRCYSBB337 - 339125 - 127
32THRCYSCC337 - 339125 - 127
42THRCYSDD337 - 339125 - 127

NCS ensembles :
ID
1
2

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Components

#1: Protein
ADAMTS-4 / / A disintegrin and metalloproteinase with thrombospondin motifs 4 / ADAM-TS 4 / ADAM-TS4 / ...A disintegrin and metalloproteinase with thrombospondin motifs 4 / ADAM-TS 4 / ADAM-TS4 / Aggrecanase-1 / ADMP-1


Mass: 34221.660 Da / Num. of mol.: 4 / Fragment: Residues 213-520 / Mutation: E362Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS4, KIAA0688 / Cell line (production host): Ovary (CHO) cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O75173, ADAMTS-4 endopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-886 / N-({4'-[(4-isobutyrylphenoxy)methyl]biphenyl-4-yl}sulfonyl)-D-valine


Mass: 509.614 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H31NO6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 4000, 0.1M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794, 0.9795, 0.9649
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2001
RadiationMonochromator: Double-crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
30.96491
ReflectionResolution: 2.8→50 Å / Num. obs: 33154 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.83 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.41

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SHARPphasing
SOLOMONphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.886 / SU B: 31.239 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1675 5.1 %RANDOM
Rwork0.206 ---
obs0.209 33138 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.067 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å20.39 Å2
2--3.66 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8592 0 160 120 8872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219005
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.96712297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60351131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99123.55369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.579151306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3311552
X-RAY DIFFRACTIONr_chiral_restr0.0720.21334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026940
X-RAY DIFFRACTIONr_nbd_refined0.20.23830
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2262
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0460.24
X-RAY DIFFRACTIONr_mcbond_it0.3191.55823
X-RAY DIFFRACTIONr_mcangle_it0.58329183
X-RAY DIFFRACTIONr_scbond_it0.80833542
X-RAY DIFFRACTIONr_scangle_it1.3094.53114
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A12TIGHT POSITIONAL0.020.05
12B12TIGHT POSITIONAL0.020.05
13C12TIGHT POSITIONAL0.020.05
14D12TIGHT POSITIONAL0.020.05
11A13MEDIUM POSITIONAL0.50.5
12B13MEDIUM POSITIONAL0.340.5
13C13MEDIUM POSITIONAL0.260.5
14D13MEDIUM POSITIONAL0.60.5
11A12TIGHT THERMAL0.050.5
12B12TIGHT THERMAL0.050.5
13C12TIGHT THERMAL0.060.5
14D12TIGHT THERMAL0.050.5
11A13MEDIUM THERMAL0.362
12B13MEDIUM THERMAL0.22
13C13MEDIUM THERMAL0.192
14D13MEDIUM THERMAL0.42
21A12TIGHT POSITIONAL0.030.05
22B12TIGHT POSITIONAL0.020.05
23C12TIGHT POSITIONAL0.010.05
24D12TIGHT POSITIONAL0.020.05
21A8MEDIUM POSITIONAL0.160.5
22B8MEDIUM POSITIONAL0.050.5
23C8MEDIUM POSITIONAL0.090.5
24D8MEDIUM POSITIONAL0.120.5
21A12TIGHT THERMAL0.090.5
22B12TIGHT THERMAL0.060.5
23C12TIGHT THERMAL0.060.5
24D12TIGHT THERMAL0.080.5
21A8MEDIUM THERMAL0.362
22B8MEDIUM THERMAL0.382
23C8MEDIUM THERMAL0.262
24D8MEDIUM THERMAL0.552
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 124 -
Rwork0.283 2303 -
all-2427 -
obs--100 %
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)
14.28180.5519-0.8161.76320.32126.6783-0.12410.1335-0.13620.01460.0674-0.11260.1598-0.04490.0567-0.2326-0.0007-0.008-0.2671-0.032-0.3257.431-0.10516.138
23.5709-0.12880.29841.72470.20365.4497-0.1043-0.15930.1140.01370.12770.0372-0.0001-0.2126-0.0234-0.259-0.04040.0274-0.12860.0332-0.274815.7499.7589.74
33.1269-0.3521.39092.2494-0.1185.12170.003-0.06180.14740.0892-0.04860.06770.0111-0.2660.0455-0.17190.0206-0.0534-0.144-0.0103-0.1536.0164.03458.889
45.39790.7777-4.67982.17451.188411.61750.1445-0.4957-0.1070.1825-0.14770.3233-0.22120.26850.0032-0.08460.01150.0250.139-0.089-0.187247.5845.16665.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA214 - 4362 - 224
2X-RAY DIFFRACTION1AA437 - 508225 - 296
3X-RAY DIFFRACTION2BB214 - 4362 - 224
4X-RAY DIFFRACTION2BB437 - 508225 - 296
5X-RAY DIFFRACTION3CC215 - 4363 - 224
6X-RAY DIFFRACTION3CC437 - 508225 - 296
7X-RAY DIFFRACTION4DD215 - 4363 - 224
8X-RAY DIFFRACTION4DD437 - 506225 - 294

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