BMRB Entry 19746

Name: Solution structure of synthetic Mamba-1 peptide
Published: 2015-01-26

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PDB ID: 2mjy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19746
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of synthetic Mamba-1 peptide

Deposition date:

2014-01-21

Original release date:

2015-01-26

Authors:

He, Yao; Wu, Fangming; Tian, Changlin

Citation:

Citation: Pan, Fei; He, Yao; Wen, Ming; Wu, Fangming; Sun, Demeng; Liu, Lei; Zhang, Longhua; Li, Yiming; Tian, Changlin. "One-pot hydrazide-based native chemical ligation for efficient chemical synthesis and structure determination of toxin Mambalgin-1" Chem. Commun. (Camb.) 50, 5837-5839 (2014).
PubMed: 24619065

Assembly members:

Assembly members:
Mamba-1, polymer, 57 residues, 6574.659 Da.

Natural source:

Natural source: Common Name: Snakes Taxonomy ID: 8624 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Dendroaspis polylepis

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Mamba-1: LKCYQHGKVVTCHRDMKFCY HNTGMPFRNLKLILQGCSSS CSETENNKCCSTDRCNK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	268

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	synthetic Mamba-1 peptide	1

Entities:

Entity 1, synthetic Mamba-1 peptide 57 residues - 6574.659 Da.

1

LEU

LYS

CYS

TYR

GLN

HIS

GLY

LYS

VAL

2

THR

CYS

HIS

ARG

ASP

MET

LYS

PHE

CYS

TYR

3

HIS

ASN

THR

GLY

MET

PRO

PHE

ARG

ASN

LEU

4

LYS

LEU

ILE

LEU

GLN

GLY

CYS

SER

5

CYS

SER

GLU

THR

GLU

ASN

LYS

CYS

6

SER

THR

ASP

ARG

CYS

ASN

LYS

Samples:

sample_1: sodium phosphate 50 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_2: sodium phosphate 50 mM; ethanol, [U-2H], 5%; H2O 90%; D2O, [U-100% 2H], 10%

sample_3: sodium phosphate 50 mM; TFE, [U-2H], 5%; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 160.8 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 160.8 mM; pH: 6.5; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_2

Software:

VNMRJ, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

SPARKY, Goddard - chemical shift assignment, data analysis

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

Molmol, Koradi, Billeter and Wuthrich - geometry optimization

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Varian INOVA 700 MHz
Varian INOVA 500 MHz

BMRB	19542
PDB	2MFA 2MJY
GB	AFT65615
SP	C0HJB0 P0DKR6 P0DKS3
AlphaFold	C0HJB0 P0DKR6 P0DKS3