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Found 1 Document (0.58 seconds)

BMRB: 25775

2N6O

Structure of spider-venom peptide Hm1a

Authors

Undheim, E.AB., King, G.F., Mobli, M.

Assembly

spider-venom peptide Hm1a

Entity

1. spider-venom peptide Hm1a (polymer, Thiol state: all disulfide bound), 35 monomers, 4003.439 Da Detail

ECRYLFGGCS STSDCCKHLS CRSDWKYCAW DGTFS

Formula weight

4003.439 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS2:SG	1:CYS16:SG
2	disulfide	sing	1:CYS9:SG	1:CYS21:SG
3	disulfide	sing	1:CYS15:SG	1:CYS28:SG

Source organism

Heteroscodra maculata

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.9 %, Completeness (bb): 85.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.9 % (347 of 386)	100.0 % (198 of 198)	74.8 % (113 of 151)	97.3 % (36 of 37)
Backbone	85.2 % (179 of 210)	100.0 % (73 of 73)	70.6 % (72 of 102)	97.1 % (34 of 35)
Sidechain	96.6 % (201 of 208)	100.0 % (125 of 125)	91.4 % (74 of 81)	100.0 % (2 of 2)
Aromatic	89.1 % (57 of 64)	100.0 % (32 of 32)	76.7 % (23 of 30)	100.0 % (2 of 2)
Methyl	100.0 % (14 of 14)	100.0 % (7 of 7)	100.0 % (7 of 7)

1. Hm1a

ECRYLFGGCS STSDCCKHLS CRSDWKYCAW DGTFS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Hm1a	natural abundance	1.0 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.1013291

Referencing offset: -0.24 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.1013291

Referencing offset: -0.24 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.77 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	4.77 ppm	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N6O, Strand ID: A Detail

Release date

2016-08-24

Citation 1

A selective Na_V1.1 activator with potential for treatment of Dravet syndrome epilepsy
Undheim, E.AB., King, G.F., Mobli, M., Petrou, S.
Biochem. Pharmacol. (2020), 113991-113991, PubMed 32335140 , DOI 10.1016/j.bcp.2020.113991 , Abstract

Show more 1 citaion

Citation 2

Novel tarantula toxins for subtypes of voltage-dependent potassium channels in the Kv2 and Kv4 subfamilies
Escoubas, P., Diochot, S., Celerier, M., Nakajima, T., Lazdunski, M.
Mol. Pharmacol. (2002), 62, 48-57, PubMed 12065754 , DOI: , Abstract

Hide non-primary 1 citaion

Related entities 1. spider-venom peptide Hm1a, : 1 : 1 : 109 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25775_2n6o.nef
Input source #2: Coordindates	2n6o.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:2:CYS:SG	A:16:CYS:SG	oxidized, CA 54.925, CB 41.735 ppm	oxidized, CA 53.616, CB 39.385 ppm	2.063
A:9:CYS:SG	A:21:CYS:SG	oxidized, CA 53.667, CB 47.288 ppm	oxidized, CA 53.379, CB 41.159 ppm	1.974
A:15:CYS:SG	A:28:CYS:SG	oxidized, CA 53.598, CB 40.96 ppm	oxidized, CA 55.737, CB 41.013 ppm	1.967

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-----
ECRYLFGGCSSTSDCCKHLSCRSDWKYCAWDGTFS
|||||||||||||||||||||||||||||||||||
ECRYLFGGCSSTSDCCKHLSCRSDWKYCAWDGTFS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_25775_2n6o.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	342		100.0 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	530 (1)	noe	100.0 (chain: A, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	56 (56)	.	100.0 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 197
  - ¹³C chemical shifts: 107
  - ¹⁵N chemical shifts: 38
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Tautomeric state of HIS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	197	99.5
¹³C chemical shifts	151	107	70.9
¹⁵N chemical shifts	39	38	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	72	98.6
¹³C chemical shifts	70	34	48.6
¹⁵N chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	125	125	100.0
¹³C chemical shifts	81	73	90.1
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	7	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	32	100.0
¹³C chemical shifts	30	22	73.3
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of restraints: 530
- Weight of restraints: 1.0 (530)
- Potential type of restraints: upper-bound-parabolic (530)
- Range of distance target values: 2.4, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Hm1a, cystine knot, gating modifier, spider venom, toxin

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Found 1 Document (0.58 seconds)

BMRB: 25775

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. spider-venom peptide Hm1a, : 1 : 1 : 109 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail