BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 5153

Title: Backbone dynamics of the N-TIMP-1 bound to MMP-3 catalytic domain

Authors: Gao, Guanghua; Arumugam, Sengodagounder; Van Doren, Steven

Citation: Gao, Guanghua; Arumugam, Sengodagounder; Patton, Brian; Semenchenko, Valentyna; Brew, Keith; Van Doren, Steven. "Binding of the MMP-3 catalytic domain to N-TIMP-1 is driven by a large gain in entropy that includes modest contributions from the hydrophobic effect and the TIMP-1 backbone"  J. Mol. Biol. ., .-..

Assembly members:
N-terminal domain of Tissue Inhibitor of Metalloproteinases-1, polymer, 126 residues, Formula weight is not available
MatrixMetalloProteinases-3(catalytic domain), polymer, 173 residues, Formula weight is not available
CA, non-polymer, 40.078 Da.
ZN, non-polymer, 65.409 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology

Entity Sequences (FASTA):
N-terminal domain of Tissue Inhibitor of Metalloproteinases-1: CTCVPPHPQTAFCNSDLVIR AKFVGTPEVNQTTLYQRYEI KMTKMYKGFQALGDAADIRF VYTPAMESVCGYFHRSHNRS EEFLIAGKLQDGLLHITTCS FVAPWNSLSLAQRRGFTKTY TVGCEE
MatrixMetalloProteinases-3(catalytic domain): FRTFPGIPKWRKTHLTYRIV NYTPDLPKDAVDSAVEKALK VWEEVTPLTFSRLYEGEADI MISFAVREHGDFYPFDGPGN VLAHAYAPGPGINGDAHFDD DEQWTKDTTGTNLFLVAAHQ IGHSLGLFHSANTEALMYPL YHSLTDLTRFRLSQDDINGI QSLYGPPPDSPET

Data sets:
Data typeCount
T1 relaxation values85
T2 relaxation values85
order parameters86

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1N-TIMP-1, inhibitor1
2MMP-3, metalloproteinase2
3CALCIUM (II) ION, I3
4CALCIUM (II) ION, II3
5CALCIUM (II) ION, III3
6ZINC (II) ION, I4
7ZINC (II) ION, II4

Entities:

Entity 1, N-TIMP-1, inhibitor 126 residues - Formula weight is not available

1   CYSTHRCYSVALPROPROHISPROGLNTHR
2   ALAPHECYSASNSERASPLEUVALILEARG
3   ALALYSPHEVALGLYTHRPROGLUVALASN
4   GLNTHRTHRLEUTYRGLNARGTYRGLUILE
5   LYSMETTHRLYSMETTYRLYSGLYPHEGLN
6   ALALEUGLYASPALAALAASPILEARGPHE
7   VALTYRTHRPROALAMETGLUSERVALCYS
8   GLYTYRPHEHISARGSERHISASNARGSER
9   GLUGLUPHELEUILEALAGLYLYSLEUGLN
10   ASPGLYLEULEUHISILETHRTHRCYSSER
11   PHEVALALAPROTRPASNSERLEUSERLEU
12   ALAGLNARGARGGLYPHETHRLYSTHRTYR
13   THRVALGLYCYSGLUGLU

Entity 2, MMP-3, metalloproteinase 173 residues - Formula weight is not available

1   PHEARGTHRPHEPROGLYILEPROLYSTRP
2   ARGLYSTHRHISLEUTHRTYRARGILEVAL
3   ASNTYRTHRPROASPLEUPROLYSASPALA
4   VALASPSERALAVALGLULYSALALEULYS
5   VALTRPGLUGLUVALTHRPROLEUTHRPHE
6   SERARGLEUTYRGLUGLYGLUALAASPILE
7   METILESERPHEALAVALARGGLUHISGLY
8   ASPPHETYRPROPHEASPGLYPROGLYASN
9   VALLEUALAHISALATYRALAPROGLYPRO
10   GLYILEASNGLYASPALAHISPHEASPASP
11   ASPGLUGLNTRPTHRLYSASPTHRTHRGLY
12   THRASNLEUPHELEUVALALAALAHISGLN
13   ILEGLYHISSERLEUGLYLEUPHEHISSER
14   ALAASNTHRGLUALALEUMETTYRPROLEU
15   TYRHISSERLEUTHRASPLEUTHRARGPHE
16   ARGLEUSERGLNASPASPILEASNGLYILE
17   GLNSERLEUTYRGLYPROPROPROASPSER
18   PROGLUTHR

Entity 3, CALCIUM (II) ION, I - Ca - 40.078 Da.

1   CA

Entity 4, ZINC (II) ION, I - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: N-terminal domain of Tissue Inhibitor of Metalloproteinases-1, [U-98% 15N; U-98% 2H], 0.3 mM; MatrixMetalloProteinases-3(catalytic domain), [U-98% 15N; U-98% 2H], 0.3 mM; Tris, [U-2H], 20 mM; NaCl 125 mM; CaCl2 10 mM; NaN3 1 mM; ZnCl2 50 mM; H2O 93%; D2O 7%

condition_1: pH: 6.22; temperature: 307 K

Experiments:

NameSampleSample stateSample conditions
15N T1 relaxationsample_1not availablecondition_1
15N T2 relaxationsample_1not availablecondition_1
heteronuclear 1H-15N NOEsample_1not availablecondition_1

Software:

Sybyl TRIAD v6.3 -

ModelFree v4.1 -

NMR spectrometers:

  • Varian Inova 600 MHz

Related Database Links:

BMRB 15120 15395 15396 4173 4364 4365 4366 5099 5231
PDB
DBJ BAD97003 BAD97011 BAG36115 BAG36115 BAD97011 BAD97003
EMBL CAA28859 CAA28859
GB AAA00036 AAA36321 AAB36942 AAD45887 AAH69676
REF NP_002413 XP_002822450 XP_003253099 XP_003828425 XP_004052086 XP_508723 XP_001154004 XP_001153941 NP_002413
SP P08254
SWISS-PROT P08254
GenBank AAH69676 AAD45887 AAB36942 AAA36321 AAA00036
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