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Found 1 Document (0.473 seconds)

BMRB: 30318

5WLX

Solution structure of kappa-theraphotoxin-Aa1a

Authors

Chin, Y.K.Y., Ma, L., King, G.F.

Assembly

Kappa-theraphotoxin-Aa1a

Entity

1. Kappa-theraphotoxin-Aa1a (polymer), 37 monomers, 4155.744 Da Detail

GDCHKFLGWC RGEKDPCCEH LTCHVKHGWC VWDGTIX

Formula weight

4155.744 Da

Source organism

Avicularia

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 86.8 %, Completeness (bb): 80.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.8 % (356 of 410)	94.8 % (200 of 211)	73.3 % (118 of 161)	100.0 % (38 of 38)
Backbone	80.8 % (173 of 214)	97.4 % (74 of 76)	62.1 % (64 of 103)	100.0 % (35 of 35)
Sidechain	93.8 % (213 of 227)	93.3 % (126 of 135)	94.4 % (84 of 89)	100.0 % (3 of 3)
Aromatic	96.8 % (60 of 62)	100.0 % (31 of 31)	92.9 % (26 of 28)	100.0 % (3 of 3)
Methyl	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)

1. entity 1

GDCHKFLGWC RGEKDPCCEH LTCHVKHGWC VWDGTIX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4 (±0.05), Details 1 mM Kappa-theraphotoxin-Aa1a, 20 mM sodium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Kappa-theraphotoxin-Aa1a	natural abundance		1 mM
2	sodium phosphate	natural abundance		20 mM

Release date

2017-08-13

Citation

Novel venom-derived inhibitors of the human EAG channel, a putative antiepileptic drug target
Ma, L., Chin, Y., Dekan, Z., Herzig, V., Chow, C.Y., Heighway, J., Lam, S.W., Guillemin, G.J., Alewood, P.F., King, G.F.
Biochem. Pharmacol. (2018), 158, 60-72, PubMed 30149017 , DOI 10.1016/j.bcp.2018.08.038 , Abstract

Related entities 1. Kappa-theraphotoxin-Aa1a, : 1 : 105 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30318_5wlx.nef
Input source #2: Coordindates	5wlx.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	True (see coodinates for details)
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:18:CYS:SG	oxidized, CA 54.322, CB 42.044 ppm	oxidized, CA 53.807, CB 39.998 ppm	2.0
A:10:CYS:SG	A:23:CYS:SG	oxidized, CA 54.127, CB 45.81 ppm	oxidized, CB 39.188 ppm	2.0
A:17:CYS:SG	A:30:CYS:SG	oxidized, CA 57.142, CB 41.279 ppm	oxidized, CA 55.962, CB 41.818 ppm	1.999

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:36:ILE:C	1:37:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	37	NH2	AMINO GROUP	Assigned chemical shifts, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------20--------30-------
GDCHKFLGWCRGEKDPCCEHLTCHVKHGWCVWDGTIX
|||||||||||||||||||||||||||||||||||||
GDCHKFLGWCRGEKDPCCEHLTCHVKHGWCVWDGTIX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	37	0	0	100.0

Content subtype: combined_30318_5wlx.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_chemical_shifts_1	Warning	370		100.0 (chain: A, length: 37)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	18 (1)	undefined	16.2 (chain: A, length: 37)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	557 (1)	noe	91.9 (chain: A, length: 37)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	312 (312)	.	100.0 (chain: A, length: 37)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 211
  - ¹³C chemical shifts: 121
  - ¹⁵N chemical shifts: 38
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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	213	211	99.1
¹³C chemical shifts	161	121	75.2
¹⁵N chemical shifts	40	38	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	75	98.7
¹³C chemical shifts	72	34	47.2
¹⁵N chemical shifts	36	35	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	136	99.3
¹³C chemical shifts	89	87	97.8
¹⁵N chemical shifts	4	3	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0
¹³C chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0
¹³C chemical shifts	28	26	92.9
¹⁵N chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 16.2%
- Total number of restraints: 18
- Weight of restraints: 1.0 (18)
- Potential type of restraints: upper-bound-parabolic (18)
- Range of distance target values: 2.0, 3.1 (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: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 91.9%
  - Total number of restraints: 557
  - Weight of restraints: 1.0 (557)
  - Potential type of restraints: upper-bound-parabolic (557)
  - Range of distance target values: 2.39, 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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of restraints: 312
- Total number of restraints per polymer type: 312
- Weight of restraints: 1.0 (312)
- Potential type of restraints: square-well-parabolic (312)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Spider toxins; Inhibitor cystine knot; Theraphotoxin, TOXIN

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Found 1 Document (0.473 seconds)

BMRB: 30318

Sample

Related entities 1. Kappa-theraphotoxin-Aa1a, : 1 : 105 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail