BMRB Entry 16416
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16416
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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
- assigned_chemical_shifts
- chemical_rates
| Data type | Count |
| binding constants | 1 |
| kinetic rates | 2 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | HIV-PR(D25N) | 1 |
| 2 | substrate C | 2 |
| 3 | HIV-PR(D25N) | 3 |
Entities:
Entity 1, HIV-PR(D25N) 99 residues - Formula weight is not available
| 1 | PRO | GLN | VAL | THR | LEU | TRP | LYS | ARG | PRO | LEU | ||||
| 2 | VAL | THR | ILE | LYS | ILE | GLY | GLY | GLN | LEU | LYS | ||||
| 3 | GLU | ALA | LEU | LEU | ASP | THR | GLY | ALA | ASP | ASP | ||||
| 4 | THR | VAL | ILE | GLU | GLU | MET | SER | LEU | PRO | GLY | ||||
| 5 | ARG | TRP | LYS | PRO | LYS | MET | ILE | GLY | GLY | ILE | ||||
| 6 | GLY | GLY | PHE | ILE | LYS | VAL | ARG | GLN | TYR | ASP | ||||
| 7 | GLN | ILE | ILE | ILE | GLU | ILE | ALA | GLY | HIS | LYS | ||||
| 8 | ALA | ILE | GLY | THR | VAL | LEU | VAL | GLY | PRO | THR | ||||
| 9 | PRO | VAL | ASN | VAL | ILE | GLY | ARG | ASN | LEU | LEU | ||||
| 10 | THR | GLN | ILE | GLY | ALA | THR | LEU | ASN | PHE |
Entity 2, substrate C 9 residues - Formula weight is not available
| 1 | LYS | ALA | ARG | VAL | NLE | PPN | GLN | ALA | NLE |
Entity 3, HIV-PR(D25N) 99 residues - Formula weight is not available
| 1 | PRO | GLN | VAL | THR | LEU | TRP | LYS | ARG | PRO | LEU | ||||
| 2 | VAL | THR | ILE | LYS | ILE | GLY | GLY | GLN | LEU | LYS | ||||
| 3 | GLU | ALA | LEU | LEU | ASN | THR | GLY | ALA | ASP | ASP | ||||
| 4 | THR | VAL | ILE | GLU | GLU | MET | SER | LEU | PRO | GLY | ||||
| 5 | ARG | TRP | LYS | PRO | LYS | MET | ILE | GLY | GLY | ILE | ||||
| 6 | GLY | GLY | PHE | ILE | LYS | VAL | ARG | GLN | TYR | ASP | ||||
| 7 | GLN | ILE | ILE | ILE | GLU | ILE | ALA | GLY | HIS | LYS | ||||
| 8 | ALA | ILE | GLY | THR | VAL | LEU | VAL | GLY | PRO | THR | ||||
| 9 | PRO | VAL | ASN | VAL | ILE | GLY | ARG | ASN | LEU | LEU | ||||
| 10 | THR | GLN | ILE | GLY | ALA | THR | LEU | ASN | PHE |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_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:
| PDB |