[English] 日本語
Yorodumi
- PDB-5boy: X-RAY Co-structure of MMP-13 with ethyl 5-(1-methyl-1H-imidazol-5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5boy
TitleX-RAY Co-structure of MMP-13 with ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-Carboxylate
ComponentsCollagenase 3
KeywordsHydrolase/Hydrolase inhibitor / Ridgefield / protease / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / 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-4UE / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsFarrow, N.A.
CitationJournal: J. Med. Chem. / Year: 2011
Title: Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13.
Authors: Taylor, S.J. / Abeywardane, A. / Liang, S. / Muegge, I. / Padyana, A.K. / Xiong, Z. / Hill-Drzewi, M. / Farmer, B. / Li, X. / Collins, B. / Li, J.X. / Heim-Riether, A. / Proudfoot, J. / ...Authors: Taylor, S.J. / Abeywardane, A. / Liang, S. / Muegge, I. / Padyana, A.K. / Xiong, Z. / Hill-Drzewi, M. / Farmer, B. / Li, X. / Collins, B. / Li, J.X. / Heim-Riether, A. / Proudfoot, J. / Zhang, Q. / Goldberg, D. / Zuvela-Jelaska, L. / Zaher, H. / Li, J. / Farrow, N.A.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Refinement description
Revision 1.2Oct 7, 2015Group: Experimental preparation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_symmetry
Remark 650HELIX DETERMINATION METHOD: MOE
Remark 700SHEET DETERMINATION METHOD: MOE

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,51114
Polymers38,4712
Non-polymers1,04112
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-138 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.079, 36.051, 95.908
Angle α, β, γ (deg.)90.00, 131.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-576-

HOH

31B-577-

HOH

-
Components

#1: Protein Collagenase 3 / / Matrix metalloproteinase-13 / MMP-13


Mass: 19235.383 Da / Num. of mol.: 2 / Fragment: UNP residues 104-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Fragment: 104-274 / Gene: MMP13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-4UE / ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-carboxylate


Mass: 269.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details404 MOL_POTENCY [IC50 in nM] 2000 CDB_METHOD_ID 18655 BRD_ID ZN2 DICTIONARY 1 0 Other ZN2 ZN ZN Zn ...404 MOL_POTENCY [IC50 in nM] 2000 CDB_METHOD_ID 18655 BRD_ID ZN2 DICTIONARY 1 0 Other ZN2 ZN ZN Zn 2 NNN 1 404 DICTIONARY 20 22 Other 404 O11 O11 O 0 NNN 1 404 C10 C10 C 0 NNN 2 404 O12 O12 O 0 NNN 3 404 C13 C13 C 0 NNN 4 404 C14 C14 C 0 NNN 5 404 C8 C8 C 0 YNN 6 404 N7 N7 N 0 YNN 7 404 C6 C6 C 0 YNN 8 404 C3 C3 C 0 YNN 9 404 C2 C2 C 0 YNN 10 404 C9 C9 C 0 YNN 11 404 C5 C5 C 0 YNN 12 404 C4 C4 C 0 YNN 13 404 C1 C1 C 0 YNN 14 404 C16 C16 C 0 YNN 15 404 N17 N17 N 0 YNN 16 404 C20 C20 C 0 NNN 17 404 C18 C18 C 0 YNN 18 404 N19 N19 N 0 YNN 19 404 C15 C15 C 0 YNN 20 404 O11 C10 DOUB NN 1 404 C10 O12 SING NN 2 404 C10 C8 SING NN 3 404 O12 C13 SING NN 4 404 C13 C14 SING NN 5 404 C8 N7 SING YN 6 404 C8 C9 DOUB YN 7 404 N7 C6 SING YN 8 404 C6 C3 DOUB YN 9 404 C6 C5 SING YN 10 404 C3 C2 SING YN 11 404 C2 C1 DOUB YN 12 404 C9 C5 SING YN 13 404 C5 C4 DOUB YN 14 404 C4 C1 SING YN 15 404 C1 C16 SING NN 16 404 C16 N17 SING YN 17 404 C16 C15 DOUB YN 18 404 N17 C20 SING NN 19 404 N17 C18 SING YN 20 404 C18 N19 DOUB YN 21 404 N19 C15 SING YN 22

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 4000, 1M Ammonimum Formate, 100 mM Tris pH 8

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.03→67.4202 Å / Num. obs: 22828 / % possible obs: 99.56 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.6
Reflection shellResolution: 2.03→2.09 Å / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 7.27 / % possible all: 63

-
Processing

SoftwareName: PHENIX / Classification: refinement
RefinementResolution: 2.03→67.4202 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.19 --
Rwork0.16 --
obs-22828 99.56 %
Refinement stepCycle: LAST / Resolution: 2.03→67.4202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 50 393 3087
LS refinement shellHighest resolution: 2.03 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more