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BMRB: 25452

2MYH

Omega-Tbo-IT1 selective inhibitor of insect calcium channels isolated from Tibellus oblongus spider venom

Authors

Altukhov, D., Bozin, T., Bocharov, E., Kozlov, S., Mikov, A.

Assembly

Omega-Tbo-IT1 Selective Inhibitor of Insect Calcium Channels

Entity

1. Omega-Tbo-IT1 Selective Inhibitor of Insect Calcium Channels (polymer, Thiol state: all disulfide bound), 41 monomers, 4340.116 Da Detail

CASKNERCGN ALYGTKGPGC CNGKCICRTV PRKGVNSCRC M

Formula weight

4340.116 Da

Entity Connection

disulfide 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS1:SG	1:CYS21:SG
2	disulfide	sing	1:CYS8:SG	1:CYS25:SG
3	disulfide	sing	1:CYS20:SG	1:CYS40:SG
4	disulfide	sing	1:CYS20:SG	1:CYS25:SG
5	disulfide	sing	1:CYS27:SG	1:CYS38:SG

Source organism

Tibellus oblongus

Exptl. method

NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 86.4 %, Completeness (bb): 77.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	86.4 % (338 of 391)	96.5 % (223 of 231)	71.9 % (115 of 160)
Backbone	77.3 % (157 of 203)	96.5 % (83 of 86)	63.2 % (74 of 117)
Sidechain	96.0 % (214 of 223)	96.6 % (140 of 145)	94.9 % (74 of 78)
Aromatic	100.0 % (8 of 8)	100.0 % (4 of 4)	100.0 % (4 of 4)
Methyl	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)

1. Omega-Tbo-IT1

CASKNERCGN ALYGTKGPGC CNGKCICRTV PRKGVNSCRC M

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Omega-Tbo-IT1	natural abundance	1.5 (±0.2) mM
2	sodium phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	30 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 285 K, pH 5.8

#	Name	Isotope labeling	Concentration
6	Omega-Tbo-IT1	natural abundance	1.5 (±0.2) mM
7	sodium phosphate buffer	natural abundance	20 mM
8	NaCl	natural abundance	30 mM
9	D2O	natural abundance	100 %

Protein Blocks Logo

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

Release date

2015-12-06

Citation

ω-Tbo-IT1-New Inhibitor of Insect Calcium Channels Isolated from Spider Venom
Mikov, A.N., Fedorova, I.M., Potapieva, N.N., Maleeva, E.E., Bocharov, E.V., Bozin, T.N., Altukhov, D.A., Lipkin, A.V., Kozlov, S.A., Tikhonov, D.B., Grishin, E.V.
Sci. Rep. (2015), 5, 17232-17232, PubMed 26611444 , DOI 10.1038/srep17232 , Abstract

Experiments performed 4 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25452_2myh.nef
Input source #2: Coordindates	2myh.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:1:CYS:SG	A:21:CYS:SG	oxidized, CA 54.258, CB 41.807 ppm	oxidized, CA 56.857, CB 39.151 ppm	1.988
A:8:CYS:SG	A:25:CYS:SG	oxidized, CA 52.465, CB 48.107 ppm	oxidized, CA 55.336, CB 38.089 ppm	2.115
A:20:CYS:SG	A:40:CYS:SG	oxidized, CA 55.904, CB 39.643 ppm	oxidized, CA 56.037, CB 39.651 ppm	1.992
A:20:CYS:SG	A:25:CYS:SG	oxidized, CA 55.904, CB 39.643 ppm	oxidized, CA 55.336, CB 38.089 ppm	2.732
A:27:CYS:SG	A:38:CYS:SG	oxidized, CA 54.607, CB 46.328 ppm	oxidized, CA 55.624, CB 48.35 ppm	1.989

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-
CASKNERCGNALYGTKGPGCCNGKCICRTVPRKGVNSCRCM
|||||||||||||||||||||||||||||||||||||||||
CASKNERCGNALYGTKGPGCCNGKCICRTVPRKGVNSCRCM

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	41	0	0	100.0

Content subtype: combined_25452_2myh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	337		97.6 (chain: A, length: 41)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	14536 (1)	noe	100.0 (chain: A, length: 41)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	12 (1)	undefined	19.5 (chain: A, length: 41)
3	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	12 (1)	undefined	19.5 (chain: A, length: 41)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	42 (1)	hbond	68.3 (chain: A, length: 41)
5	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	42 (1)	hbond	68.3 (chain: A, length: 41)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	180 (174)	.	95.1 (chain: A, length: 41)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 223
  - ¹³C chemical shifts: 114
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	231	223	96.5
¹³C chemical shifts	160	114	71.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	83	96.5
¹³C chemical shifts	82	40	48.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	145	140	96.6
¹³C chemical shifts	78	74	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	12	92.3
¹³C chemical shifts	13	12	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	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: 41, Sequence coverage: 100.0%
- Total number of restraints: 14498
- Weight of restraints: 1.0 (14498)
- Potential type of restraints: upper-bound-parabolic (14498)
- 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
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 19.5%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: upper-bound-parabolic (12)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_7
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 19.5%
    - Total number of restraints: 12
    - Weight of restraints: 1.0 (12)
    - Potential type of restraints: upper-bound-parabolic (12)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of 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: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 68.3%
        --------10--------20--------30--------40- CASKNERCGNALYGTKGPGCCNGKCICRTVPRKGVNSCRCM || || |||||||| || | | | | || || |||||| .AS.NE.CGNALYGT..PG.C..K.I.R.VP.KG.NSCRCM
      - Total number of restraints: 42
        Total hydrogen bond restraints: 42
        O...H-x: 10
        O...h-N: 10
        Long range: 22
        O...H-x: 11
        O...h-N: 11
      - Weight of restraints: 1.0 (42)
        Total hydrogen bond restraints: 1.0 (42)
        O...H-x: 1.0 (10)
        O...h-N: 1.0 (10)
        Long range: 1.0 (22)
        O...H-x: 1.0 (11)
        O...h-N: 1.0 (11)
      - Potential type of restraints: upper-bound-parabolic (42)
        Total hydrogen bond restraints: upper-bound-parabolic (42)
        O...H-x: upper-bound-parabolic (10)
        O...h-N: upper-bound-parabolic (10)
        Long range: upper-bound-parabolic (22)
        O...H-x: upper-bound-parabolic (11)
        O...h-N: upper-bound-parabolic (11)
      - Range of distance target values: 2.0, 3.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
      - Saveframe: DYANA/DIANA_distance_constraints_6
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 68.3%
        --------10--------20--------30--------40- CASKNERCGNALYGTKGPGCCNGKCICRTVPRKGVNSCRCM || || |||||||| || | | | | || || |||||| .AS.NE.CGNALYGT..PG.C..K.I.R.VP.KG.NSCRCM
        Total number of restraints: 42
        Total hydrogen bond restraints: 42
        O...H-x (too close!): 10
        O...h-N (too close!): 10
        Long range: 22
        O...H-x (too close!): 11
        O...h-N (too close!): 11
        Weight of restraints: 1.0 (42)
        Total hydrogen bond restraints: 1.0 (42)
        O...H-x (too close!): 1.0 (10)
        O...h-N (too close!): 1.0 (10)
        Long range: 1.0 (22)
        O...H-x (too close!): 1.0 (11)
        O...h-N (too close!): 1.0 (11)
        Potential type of restraints: upper-bound-parabolic (42)
        Total hydrogen bond restraints: upper-bound-parabolic (42)
        O...H-x (too close!): upper-bound-parabolic (10)
        O...h-N (too close!): upper-bound-parabolic (10)
        Long range: upper-bound-parabolic (22)
        O...H-x (too close!): upper-bound-parabolic (11)
        O...h-N (too close!): upper-bound-parabolic (11)
        Range of distance target values: 1.8, 2.7 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 95.1%
- Total number of restraints: 174
- Total number of restraints per polymer type: 174
- Weight of restraints: 1.0 (174)
- Potential type of restraints: square-well-parabolic (174)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CYS knot, ICK, cystine knot, inhibitor cystine knot

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Found 1 Document (0.65 seconds)

BMRB: 25452

Sample #1

Sample #2

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail