Entry STF0008
Cobrotoxin (CBTX)
Protein information
| Name of the protein: | Cobrotoxin |
| Organism: | Naja atra |
| Number of residues: | 62 |
| Related UniProt entry: | P60770 (Fragment: 22 - 83) |
| Related PDB entry: | 1COE |
Visualize the data
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Experiment sets
EARLY
Method: Quenched-flow HDX NMR
Conditions: pH 3.0; 5.0 Celsius; Probes: 24
Related publication:
PMID 16497267
Experiment details: "All experiments were carried out at 5C using a RQF-63 rapid mixing quenched-flow apparatus. Complete denaturation and exchange of the backbone amide protons with deuterium was achieved by dissolving CBTX (20 mg/mL) in 6 M urea-d4 in D2O at pD 2.7. Refolding of denatured protein was initiated by a 11-fold dilution with 50 mM glycine-d5 (pH 3.0) in H2O. At this pH, H/D exchange rate was negligible. After variable refolding times ranging from 9.8 to 500 ms, the solution was diluted again to 11 times of the initial protein volume with 0.2 M sodium borate (pH 9.5) to initiate labeling of the deuterated amides in CBTX with protons."
Protection threshold: refolding time constant < 20
Sequence:
LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN
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EARLY residues
28: R;
45: S;
50: I;
53: N;
55: C;
62: N;
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INTERMEDIATE
Method: Quenched-flow HDX NMR
Conditions: pH 3.0; 5.0 Celsius; Probes: 24
Related publication:
PMID 16497267
Experiment details: "All experiments were carried out at 5C using a RQF-63 rapid mixing quenched-flow apparatus. Complete denaturation and exchange of the backbone amide protons with deuterium was achieved by dissolving CBTX (20 mg/mL) in 6 M urea-d4 in D2O at pD 2.7. Refolding of denatured protein was initiated by a 11-fold dilution with 50 mM glycine-d5 (pH 3.0) in H2O. At this pH, H/D exchange rate was negligible. After variable refolding times ranging from 9.8 to 500 ms, the solution was diluted again to 11 times of the initial protein volume with 0.2 M sodium borate (pH 9.5) to initiate labeling of the deuterated amides in CBTX with protons."
Protection threshold: 20 < refolding time constant < 40
Sequence:
LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN
CLICK TO DOWNLOAD SEQUENCE IN FASTA
INTERMEDIATE residues
6: Q;
14: T;
15: T;
26: K;
27: K;
33: R;
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LATE
Method: Quenched-flow HDX NMR
Conditions: pH 3.0; 5.0 Celsius; Probes: 24
Related publication:
PMID 16497267
Experiment details: "All experiments were carried out at 5C using a RQF-63 rapid mixing quenched-flow apparatus. Complete denaturation and exchange of the backbone amide protons with deuterium was achieved by dissolving CBTX (20 mg/mL) in 6 M urea-d4 in D2O at pD 2.7. Refolding of denatured protein was initiated by a 11-fold dilution with 50 mM glycine-d5 (pH 3.0) in H2O. At this pH, H/D exchange rate was negligible. After variable refolding times ranging from 9.8 to 500 ms, the solution was diluted again to 11 times of the initial protein volume with 0.2 M sodium borate (pH 9.5) to initiate labeling of the deuterated amides in CBTX with protons."
Protection threshold: 40 < refolding time constant < 60
Sequence:
LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN
CLICK TO DOWNLOAD SEQUENCE IN FASTA
LATE residues
2: E;
10: Q;
17: C;
24: C;
25: Y;
29: W;
30: R;
58: D;
61: N;
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STRONG
Method: Native exchange NMR
Conditions: pH 3.4; 25.0 Celsius; Probes: 38
Related publication:
PMID 10913281
Experiment details: "H/D exchange measurements in CTX III and CBTX were monitored using the magnitude COSY spectra recorded at 25°C (pH 3.4) using a Bruker DMX-600 NMR spectrometer. The samples for exchange kinetics of the amide protons in the proteins (CBTX and CTX III) were prepared by dissolving the lyophilized proteins in deuterated buffer at pD 3.6. The concentrations of the proteins (CBTX and CTX III) were 2.0 mM."
Protection threshold: log(P) > 2
Sequence:
LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN
CLICK TO DOWNLOAD SEQUENCE IN FASTA
STRONG residues
3: C;
6: Q;
9: S;
14: T;
15: T;
24: C;
25: Y;
26: K;
27: K;
29: W;
35: Y;
38: E;
39: R;
42: G;
53: N;
55: C;
59: R;
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MEDIUM
Method: Native exchange NMR
Conditions: pH 3.4; 25.0 Celsius; Probes: 38
Related publication:
PMID 10913281
Experiment details: "H/D exchange measurements in CTX III and CBTX were monitored using the magnitude COSY spectra recorded at 25°C (pH 3.4) using a Bruker DMX-600 NMR spectrometer. The samples for exchange kinetics of the amide protons in the proteins (CBTX and CTX III) were prepared by dissolving the lyophilized proteins in deuterated buffer at pD 3.6. The concentrations of the proteins (CBTX and CTX III) were 2.0 mM."
Protection threshold: 1 < log(P) < 2
Sequence:
LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN
CLICK TO DOWNLOAD SEQUENCE IN FASTA
MEDIUM residues
2: E;
17: C;
21: E;
28: R;
30: R;
37: T;
41: C;
48: N;
50: I;
51: E;
52: I;
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