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BMRB: 19542

2MFA

Mambalgin-2

Authors

Schroeder, C.I., Rash, L.D., Vilas-Farr s, X., Rosengren, J., Mobli, M., King, G.F., Alewood, P.F., Craik, D.J., Durek, T.

Assembly

Mambalgin-2

Entity

1. Mambalgin-2 (polymer, Thiol state: all disulfide bound), 57 monomers, 6546.545 Da Detail

LKCFQHGKVV TCHRDMKFCY HNTGMPFRNL KLILQGCSSS CSETENNKCC STDRCNK

Formula weight

6546.545 Da

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.0 %, Completeness (bb): 83.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.0 % (543 of 662)	94.6 % (330 of 349)	61.6 % (154 of 250)	93.7 % (59 of 63)
Backbone	83.5 % (284 of 340)	99.1 % (115 of 116)	68.5 % (115 of 168)	96.4 % (54 of 56)
Sidechain	83.2 % (313 of 376)	92.3 % (215 of 233)	68.4 % (93 of 136)	71.4 % (5 of 7)
Aromatic	46.0 % (23 of 50)	92.0 % (23 of 25)	0.0 % (0 of 25)
Methyl	94.4 % (34 of 36)	100.0 % (18 of 18)	88.9 % (16 of 18)

1. entity

LKCFQHGKVV TCHRDMKFCY HNTGMPFRNL KLILQGCSSS CSETENNKCC STDRCNK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.6, Details Synthetic material

#	Name	Isotope labeling	Type	Concentration
1	Mambalgin-2	natural abundance		0.2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.15 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MFA, Strand ID: A Detail

Release date

2014-01-01

Citation

Chemical synthesis, 3D structure, and ASIC binding site of the toxin mambalgin-2
Schroeder, C.I., Rash, L.D., Vila-Farres, X., Rosengren, K., Mobli, M., King, G.F., Alewood, P.F., Craik, D.J., Durek, T.
Angew. Chem Int Ed Engl. (2014), 53, 1017-1020, PubMed 24323786 , DOI 10.1002/anie.201308898 , Abstract

Related entities 1. Mambalgin-2, : 1 : 1 : 7 : 91 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.6, Details Synthetic material

#	Name	Isotope labeling	Type	Concentration
1	Mambalgin-2	natural abundance		0.2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.6, Details Synthetic material

#	Name	Isotope labeling	Type	Concentration
1	Mambalgin-2	natural abundance		0.2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.6, Details Synthetic material

#	Name	Isotope labeling	Type	Concentration
1	Mambalgin-2	natural abundance		0.2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.6, Details Synthetic material

#	Name	Isotope labeling	Type	Concentration
1	Mambalgin-2	natural abundance		0.2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.6, Details Synthetic material

#	Name	Isotope labeling	Type	Concentration
1	Mambalgin-2	natural abundance		0.2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
4	Mambalgin-2	natural abundance		0.2 mM
5	D2O	natural abundance		100 %

7 2D ECOSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
4	Mambalgin-2	natural abundance		0.2 mM
5	D2O	natural abundance		100 %

8 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
4	Mambalgin-2	natural abundance		0.2 mM
5	D2O	natural abundance		100 %

9 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 3.6

#	Name	Isotope labeling	Type	Concentration
4	Mambalgin-2	natural abundance		0.2 mM
5	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19542_2mfa.nef
Input source #2: Coordindates	2mfa.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:3:CYS:SG	A:19:CYS:SG	oxidized, CA 51.272, CB 42.039 ppm	oxidized, CA 52.258, CB 38.627 ppm	2.021
A:12:CYS:SG	A:37:CYS:SG	oxidized, CA 53.036, CB 38.892 ppm	oxidized, CA 55.955, CB 48.202 ppm	2.023
A:41:CYS:SG	A:49:CYS:SG	oxidized, CA 57.567, CB 40.0 ppm	oxidized, CA 53.386, CB 44.935 ppm	2.024
A:50:CYS:SG	A:55:CYS:SG	oxidized, CA 55.983, CB 46.111 ppm	oxidized, CA 57.814, CB 46.236 ppm	2.014

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50-------
LKCFQHGKVVTCHRDMKFCYHNTGMPFRNLKLILQGCSSSCSETENNKCCSTDRCNK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LKCFQHGKVVTCHRDMKFCYHNTGMPFRNLKLILQGCSSSCSETENNKCCSTDRCNK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	57	0	0	100.0

Content subtype: combined_19542_2mfa.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	532		100.0 (chain: A, length: 57)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1271 (1)	noe	100.0 (chain: A, length: 57)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	32 (1)	hbond	38.6 (chain: A, length: 57)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	78 (78)	.	93.0 (chain: A, length: 57)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 331
  - ¹³C chemical shifts: 143
  - ¹⁵N chemical shifts: 58
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 100.0%
- Total number of restraints: 1245
- Weight of restraints: 1.0 (1245)
- Potential type of restraints: square-well-parabolic (1245)
- Range of distance target values: 1.19, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 38.6%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: square-well-parabolic (32)
  - Range of distance target values: 0.85, 1.6 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 93.0%
- Total number of restraints: 78
- Total number of restraints per polymer type: 78
- Weight of restraints: 1.0 (78)
- Potential type of restraints: square-well-parabolic (78)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Mamba, Snake, Three-finger toxin, Toxin