[English] 日本語
Yorodumi
- SASDFQ4: Domain-stapled mutant of Pro-Matrix metalloproteinase-1 (proMMP-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFQ4
SampleDomain-stapled mutant of Pro-Matrix metalloproteinase-1 (proMMP-1 S243C, S318C)
  • Pro-matrix metalloproteinase-1 (Interstitial collagenase) (proMMP-1 S243C, S318C) (protein), ProMMP-1 (S243C, S31, Homo sapiens
Function / homology
Function and homology information


interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization ...interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / serine-type endopeptidase activity / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Interstitial collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Rob Holland (University of Portsmouth)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Domain-stapled mutant of Pro-Matrix metalloproteinase-1 (proMMP-1 S243C, S318C)
Specimen concentration: 5.6 mg/ml
BufferName: 50 mM Tris-HCl, 150 mM Sodium chloride, 10 mM Calcium chloride
pH: 7.4
Entity #1573Name: ProMMP-1 (S243C, S31 / Type: protein
Description: Pro-matrix metalloproteinase-1 (Interstitial collagenase) (proMMP-1 S243C, S318C)
Formula weight: 52.007 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P03956
Sequence: MFPATLETQE QDVDLVQKYL EKYYNLKNDG RQVEKRRNSG PVVEKLKQMQ EFFGLKVTGK PDAETLKVMK QPRCGVPDVA QFVLTEGNPR WEQTHLTYRI ENYTPDLPRA DVDHAIEKAF QLWSNVTPLT FTKVSEGQAD IMISFVRGDH RDNSPFDGPG GNLAHAFQPG ...Sequence:
MFPATLETQE QDVDLVQKYL EKYYNLKNDG RQVEKRRNSG PVVEKLKQMQ EFFGLKVTGK PDAETLKVMK QPRCGVPDVA QFVLTEGNPR WEQTHLTYRI ENYTPDLPRA DVDHAIEKAF QLWSNVTPLT FTKVSEGQAD IMISFVRGDH RDNSPFDGPG GNLAHAFQPG PGIGGDAHFD EDERWTNNFR EYNLHRVAAH ELGHSLGLSH STDIGALMYP SYTFCGDVQL AQDDIDGIQA IYGRSQNPVQ PIGPQTPKAC DSKLTFDAIT TIRGEVMFFK DRFYMRTNPF YPEVELNFIC VFWPQLPNGL EAAYEFADRD EVRFFKGNKY WAVQGQNVLH GYPKDIYSSF GFPRTVKHID AALSEENTGK TYFFVANKYW RYDEYKRSMD PGYPKMIAHD FPGIGHKVDA VFMKDGFFYF FHGTRQYKFD PKTKRILTLQ KANSWFNCRK N

-
Experimental information

BeamInstrument name: Diamond Light Source B21 / City: Oxfordshire / 国: UK / Shape: 1 x 5 mm / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 3.9 mm
DetectorName: Pilatus 2M
Scan
Title: Domain-stapled mutant of Pro-Matrix metalloproteinase-1 (proMMP-1 S243C, S318C)
Measurement date: May 21, 2015 / Storage temperature: 4 °C / Cell temperature: 25 °C / Exposure time: 3 sec. / Number of frames: 28 / Unit: 1/A /
MinMax
Q0.0033 0.4038
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 866 /
MinMax
Q0.0126242 0.250388
P(R) point1 866
R0 89
Result
Type of curve: sec /
ExperimentalPorod
MW39.35 kDa38 kDa
Volume-61 nm3

P(R)GuinierGuinier error
Forward scattering, I00.01028 0.01029 5.1E-5
Radius of gyration, Rg2.71 nm2.694 nm0.021

MinMax
D-8.9
Guinier point35 164

+
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