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- PDB-3q2h: Adamts1 in complex with N-hydroxyformamide inhibitors of ADAM-TS4 -

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Basic information

Entry
Database: PDB / ID: 3q2h
TitleAdamts1 in complex with N-hydroxyformamide inhibitors of ADAM-TS4
ComponentsA disintegrin and metalloproteinase with thrombospondin motifs 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Adamts1 Zn-Metalloprotease / disintegrin / metalloproteinase / thrombospondin motifs / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / positive regulation of vascular associated smooth muscle cell migration / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / positive regulation of vascular associated smooth muscle cell migration / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / negative regulation of angiogenesis / extracellular matrix / kidney development / integrin-mediated signaling pathway / metalloendopeptidase activity / metallopeptidase activity / heparin binding / cytoplasmic vesicle / negative regulation of cell population proliferation / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M12B, ADAM-TS1 / 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-TS1 / 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 / Peptidase M12B, propeptide / Reprolysin family propeptide / 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
: / NICKEL (II) ION / Chem-QHF / A disintegrin and metalloproteinase with thrombospondin motifs 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsGerhardt, S. / Hargreaves, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: The design and synthesis of novel N-hydroxyformamide inhibitors of ADAM-TS4 for the treatment of osteoarthritis
Authors: De Savi, C. / Pape, A. / Cumming, J.G. / Ting, A. / Smith, P.D. / Burrows, J.N. / Mills, M. / Davies, C. / Lamont, S. / Milne, D. / Cook, C. / Moore, P. / Sawyer, Y. / Gerhardt, S.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_asym_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

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Assembly

Deposited unit
A: A disintegrin and metalloproteinase with thrombospondin motifs 1
B: A disintegrin and metalloproteinase with thrombospondin motifs 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,74731
Polymers65,1572
Non-polymers2,59029
Water1,76598
1
A: A disintegrin and metalloproteinase with thrombospondin motifs 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,11619
Polymers32,5791
Non-polymers1,53718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A disintegrin and metalloproteinase with thrombospondin motifs 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,63212
Polymers32,5791
Non-polymers1,05311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.859, 63.328, 110.844
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein A disintegrin and metalloproteinase with thrombospondin motifs 1 / ADAMTS-1


Mass: 32578.551 Da / Num. of mol.: 2 / Fragment: residues in UNP 256-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9UHI8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 7 types, 127 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-QHF / N-[(2S,4S)-1-({4-[2-(3,5-dimethyl-1,2-oxazol-4-yl)ethyl]piperidin-1-yl}sulfonyl)-4-(5-fluoropyrimidin-2-yl)-2-methylpentan-2-yl]-N-hydroxyformamide


Mass: 511.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34FN5O5S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.74 Å3/Da / Density % sol: 55.09 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorDate: Jan 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→36.01 Å / Num. obs: 29956 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 %
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 4.75 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIH

2jih


Resolution: 2.33→27.7 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.526 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 1514 5.1 %RANDOM
Rwork0.23625 ---
obs0.23928 28426 98.64 %-
all-28426 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 118.44 Å2 / Biso mean: 84.85 Å2 / Biso min: 40.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20.51 Å2
2--3.47 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.33→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 97 98 4545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214538
X-RAY DIFFRACTIONr_bond_other_d0.0010.022933
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9516173
X-RAY DIFFRACTIONr_angle_other_deg0.953.0077154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0835557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77524.95202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32815714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.271515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
X-RAY DIFFRACTIONr_nbd_refined0.2360.21139
X-RAY DIFFRACTIONr_nbd_other0.1970.23091
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22185
X-RAY DIFFRACTIONr_nbtor_other0.0870.22288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0710.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6361.52814
X-RAY DIFFRACTIONr_mcbond_other0.1161.51137
X-RAY DIFFRACTIONr_mcangle_it1.20624528
X-RAY DIFFRACTIONr_scbond_it1.87531786
X-RAY DIFFRACTIONr_scangle_it2.9434.51645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 92 -
Rwork0.294 1839 -
all-1931 -
obs--87.06 %
Refinement TLS params.Method: refined / Origin x: 23.1783 Å / Origin y: -0.182 Å / Origin z: 28.3634 Å
111213212223313233
T-0.1847 Å20.082 Å20.0267 Å2--0.0303 Å2-0.0747 Å2---0.1068 Å2
L0.8649 °20.2398 °20.4741 °2-1.427 °20.9357 °2--2.6761 °2
S-0.0913 Å °-0.4863 Å °-0.0003 Å °-0.004 Å °-0.0532 Å °0.1118 Å °-0.0284 Å °-0.1494 Å °0.1446 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 299
2X-RAY DIFFRACTION1B4 - 300

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