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Found 1 Document (0.555 seconds)

BMRB: 25917

2N9T

ProTx-II

Authors

Schroeder, C.I.

Assembly

ProTx-II

Entity

1. ProTx-II (polymer), 30 monomers, 3832.629 Da Detail

YCQKWMWTCD SERKCCEGMV CRLWCKKKLW

Formula weight

3832.629 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 79.0 %, Completeness (bb): 80.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.0 % (309 of 391)	91.3 % (190 of 208)	58.1 % (86 of 148)	94.3 % (33 of 35)
Backbone	80.6 % (145 of 180)	93.4 % (57 of 61)	67.4 % (60 of 89)	93.3 % (28 of 30)
Sidechain	80.4 % (193 of 240)	90.5 % (133 of 147)	62.5 % (55 of 88)	100.0 % (5 of 5)
Aromatic	44.6 % (25 of 56)	75.0 % (21 of 28)	0.0 % (0 of 24)	100.0 % (4 of 4)
Methyl	85.7 % (12 of 14)	100.0 % (7 of 7)	71.4 % (5 of 7)

1. entity

YCQKWMWTCD SERKCCEGMV CRLWCKKKLW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5 (±.5)

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	2 mg
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5 (±.5)

#	Name	Isotope labeling	Type	Concentration
4	entity	natural abundance		2 mg
5	D2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N9T, Strand ID: A Detail

Release date

2016-07-04

Citation

Interaction of Tarantula Venom Peptide ProTx-II with Lipid Membranes is a Prerequisite for its Inhibition of Human Voltage-gated Sodium Channel NaV1.7
Henriques, S.T., Deplazes, E., Lawrence, N., Chenval, O., Inserra, M., Thongyoo, P., Marks, A.E., Vetter, I., Craik, D.J., Schroeder, C.I.
J. Biol. Chem. (2016), 291, 17049-17065, PubMed 27311819 , DOI 10.1074/jbc.M116.729095 , Abstract

Related entities 1. ProTx-II, : 1 : 5 : 1 : 2 : 23 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25917_2n9t.nef
Input source #2: Coordindates	2n9t.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 51.805, CB 40.451 ppm	oxidized, CA 51.362, CB 37.233 ppm	2.026
A:9:CYS:SG	A:21:CYS:SG	oxidized, CA 50.915, CB 45.428 ppm	oxidized, CA 52.509, CB 37.078 ppm	2.034
A:15:CYS:SG	A:25:CYS:SG	oxidized, CA 53.093, CB 38.004 ppm	oxidized, CA 53.656, CB 37.264 ppm	2.007

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
YCQKWMWTCDSERKCCEGMVCRLWCKKKLW
||||||||||||||||||||||||||||||
YCQKWMWTCDSERKCCEGMVCRLWCKKKLW

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	30	0	0	100.0

Content subtype: combined_25917_2n9t.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	321		100.0 (chain: A, length: 30)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	492 (1)	noe	100.0 (chain: A, length: 30)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	5 (1)	hbond	26.7 (chain: A, length: 30)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	38 (38)	.	90.0 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 204
  - ¹³C chemical shifts: 84
  - ¹⁵N chemical shifts: 33
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
14	LYS	HZ1	7.549
14	LYS	HZ2	7.549
14	LYS	HZ3	7.549
26	LYS	HZ1	7.61
26	LYS	HZ2	7.61
26	LYS	HZ3	7.61
27	LYS	HZ1	7.448
27	LYS	HZ2	7.448
27	LYS	HZ3	7.448
28	LYS	HZ1	7.443
28	LYS	HZ2	7.443
28	LYS	HZ3	7.443

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	192	92.3
¹³C chemical shifts	148	84	56.8
¹⁵N chemical shifts	37	33	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	60	98.4
¹³C chemical shifts	60	30	50.0
¹⁵N chemical shifts	30	28	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	132	89.8
¹³C chemical shifts	88	54	61.4
¹⁵N chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	7	77.8
¹³C chemical shifts	9	5	55.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	21	75.0
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	4	4	100.0

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: 30, Sequence coverage: 100.0%
- Total number of restraints: 492
- Weight of restraints: 1.0 (492)
- Potential type of restraints: square-well-parabolic (492)
- Range of distance target values: 1.28, 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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 26.7%
  - Total number of restraints: 5
  - Weight of restraints: 1.0 (5)
  - Potential type of restraints: square-well-parabolic (5)
  - Range of distance target values: 1.65, 1.65 (Å)
  - 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: 30, Sequence coverage: 90.0%
- Total number of restraints: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Cystine knot, Peptide, Spider, Toxin

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Found 1 Document (0.555 seconds)

BMRB: 25917

Sample #1

Sample #2

Related entities 1. ProTx-II, : 1 : 5 : 1 : 2 : 23 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail