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 16416

Title: A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex   PubMed: 12824484

Deposition date: 2009-07-23 Original release date: 2012-06-06

Authors: Katoh, Etsuko; Louis, John; Yamazaki, Toshimasa; Gronenborn, Angela; Torchia, Dennis; Ishima, Rieko

Citation: Katoh, Etsuko; Louis, John; Yamazaki, Toshimasa; Gronenborn, Angela; Torchia, Dennis; Ishima, Rieko. "A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex."  Protein Sci. 12, 1376-1385 (2003).

Assembly members:
HIV-PR, polymer, 99 residues, Formula weight is not available
substrate_C, polymer, 9 residues, Formula weight is not available
HIV-PR(D25N), polymer, 99 residues, Formula weight is not available

Natural source:   Common Name: HIV   Taxonomy ID: 12721   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
HIV-PR: PQVTLWKRPLVTIKIGGQLK EALLDTGADDTVIEEMSLPG RWKPKMIGGIGGFIKVRQYD QIIIEIAGHKAIGTVLVGPT PVNVIGRNLLTQIGATLNF
substrate_C: KARVXXQAX
HIV-PR(D25N): PQVTLWKRPLVTIKIGGQLK EALLNTGADDTVIEEMSLPG RWKPKMIGGIGGFIKVRQYD QIIIEIAGHKAIGTVLVGPT PVNVIGRNLLTQIGATLNF

Data sets:
Data typeCount
binding constants1
kinetic rates2

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1HIV-PR(D25N)1
2substrate C2
3HIV-PR(D25N)3

Entities:

Entity 1, HIV-PR(D25N) 99 residues - Formula weight is not available

1   PROGLNVALTHRLEUTRPLYSARGPROLEU
2   VALTHRILELYSILEGLYGLYGLNLEULYS
3   GLUALALEULEUASPTHRGLYALAASPASP
4   THRVALILEGLUGLUMETSERLEUPROGLY
5   ARGTRPLYSPROLYSMETILEGLYGLYILE
6   GLYGLYPHEILELYSVALARGGLNTYRASP
7   GLNILEILEILEGLUILEALAGLYHISLYS
8   ALAILEGLYTHRVALLEUVALGLYPROTHR
9   PROVALASNVALILEGLYARGASNLEULEU
10   THRGLNILEGLYALATHRLEUASNPHE

Entity 2, substrate C 9 residues - Formula weight is not available

1   LYSALAARGVALNLEPPNGLNALANLE

Entity 3, HIV-PR(D25N) 99 residues - Formula weight is not available

1   PROGLNVALTHRLEUTRPLYSARGPROLEU
2   VALTHRILELYSILEGLYGLYGLNLEULYS
3   GLUALALEULEUASNTHRGLYALAASPASP
4   THRVALILEGLUGLUMETSERLEUPROGLY
5   ARGTRPLYSPROLYSMETILEGLYGLYILE
6   GLYGLYPHEILELYSVALARGGLNTYRASP
7   GLNILEILEILEGLUILEALAGLYHISLYS
8   ALAILEGLYTHRVALLEUVALGLYPROTHR
9   PROVALASNVALILEGLYARGASNLEULEU
10   THRGLNILEGLYALATHRLEUASNPHE

Samples:

sample_1: HIV-PR(D25N), [U-15N], 0.2 mM; substrate C 6 mM; sodium phosphate 20 mM

sample_2: HIV-PR, [U-15N], 0.2 mM; substrate C 6 mM; sodium phosphate 20 mM

sample_conditions_1: pH: 5.8; pressure: 1 atm; temperature: 293.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

ModelFree, Palmer - chemical exchange contribution to T2, order parameter identification

NMR spectrometers:

  • Bruker DMX 500 MHz
  • Bruker DMX 750 MHz

Related Database Links:

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