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BMRB: 15983

2K9E

NMR SOLUTION STRUCTURE FOR ShK-192: A POTENT KV1.3-SPECIFIC IMMUNOSUPPRESSIVE POLYPEPTIDE

Authors

Galea, C.A.

Assembly

ShK-192

Entity

1. ShK-192 (polymer, Thiol state: all disulfide bound), 37 monomers, 4414.104 Da Detail

XRSCIDTIPK SRCTAFQCKH SXKYRLSFCR KTCGTCX

Formula weight

4414.104 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS36:SG
2	disulfide	sing	1:CYS13:SG	1:CYS29:SG
3	disulfide	sing	1:CYS18:SG	1:CYS33:SG

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.9 %, Completeness: 67.8 %, Completeness (bb): 64.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.8 % (269 of 397)	95.7 % (201 of 210)	24.2 % (37 of 153)	91.2 % (31 of 34)
Backbone	64.9 % (131 of 202)	94.1 % (64 of 68)	35.6 % (36 of 101)	93.9 % (31 of 33)
Sidechain	61.4 % (140 of 228)	96.5 % (137 of 142)	3.5 % (3 of 85)	0.0 % (0 of 1)
Aromatic	50.0 % (16 of 32)	100.0 % (16 of 16)	0.0 % (0 of 16)
Methyl	40.9 % (9 of 22)	81.8 % (9 of 11)	0.0 % (0 of 11)

1. ShK-192

XRSCIDTIPK SRCTAFQCKH SXKYRLSFCR KTCGTCX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details 3 mM ShK-192, pH 4.97

#	Name	Isotope labeling	Concentration
1	ShK-192	natural abundance	3.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details ShK-192, 3.0 mM, pH 4.1

#	Name	Isotope labeling	Concentration
5	ShK-192	natural abundance	3.0 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	10 mM
8	sodium acetate	natural abundance	10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2K9E, Strand ID: A Detail

Release date

2009-04-01

Citation

Engineering a stable and selective peptide blocker of the Kv1.3 channel in T lymphocytes
Pennington, M.W., Beeton, C., Galea, C.A., Smith, B.J., Chi, V., Monaghan, K.P., Garcia, A., Rangaraju, S., Giuffrida, A., Plank, D., Crossley, G., Nugent, D., Khaytin, I., LeFievre, Y., Peshenko, I., Dixon, C., Chauhan, S., Orzel, A., Inoue, T., Hu, X., Moore, R.V., Norton, R.S., Chandy, K.G.
Mol. Pharmacol. (2009), 75, 762-773, PubMed 19122005 , DOI 10.1124/mol.108.052704 , Abstract

Related entities 1. ShK-192, : 1 : 11 : 17 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details 3 mM ShK-192, pH 4.97

#	Name	Isotope labeling	Concentration
1	ShK-192	natural abundance	3.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	10 mM

2 2D 1H-13C HSQC

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details 3 mM ShK-192, pH 4.97

#	Name	Isotope labeling	Concentration
1	ShK-192	natural abundance	3.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	10 mM

3 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details 3 mM ShK-192, pH 4.97

#	Name	Isotope labeling	Concentration
1	ShK-192	natural abundance	3.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	10 mM

4 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 278 K, pH 4.1, Details ShK-192, 3.0 mM, pH 4.1

#	Name	Isotope labeling	Concentration
5	ShK-192	natural abundance	3.0 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	10 mM
8	sodium acetate	natural abundance	10 mM

5 2D 1H-13C HSQC

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 278 K, pH 4.1, Details ShK-192, 3.0 mM, pH 4.1

#	Name	Isotope labeling	Concentration
5	ShK-192	natural abundance	3.0 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	10 mM
8	sodium acetate	natural abundance	10 mM

6 2D 1H-1H COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details 3 mM ShK-192, pH 4.97

#	Name	Isotope labeling	Concentration
1	ShK-192	natural abundance	3.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	10 mM

7 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4.79, Details 3 mM ShK-192, pH 4.97

#	Name	Isotope labeling	Concentration
1	ShK-192	natural abundance	3.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	10 mM

8 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 278 K, pH 4.1, Details ShK-192, 3.0 mM, pH 4.1

#	Name	Isotope labeling	Concentration
5	ShK-192	natural abundance	3.0 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	10 mM
8	sodium acetate	natural abundance	10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15983_2k9e.nef
Input source #2: Coordindates	2k9e.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:35:CYS:SG	unknown, CA 53.66 ppm	unknown, CA 54.59 ppm	2.02
A:12:CYS:SG	A:28:CYS:SG	unknown, CA 56.25 ppm	unknown, CA 54.17 ppm	2.021
A:17:CYS:SG	A:32:CYS:SG	unknown, CA 57.13 ppm	unknown, CA 55.24 ppm	2.017

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)
1:1:PFX:C	1:2:ARG:N	unknown	unknown	n/a
1:21:SER:C	1:22:NLE:N	unknown	unknown	n/a
1:22:NLE:C	1:23:LYS:N	unknown	unknown	n/a
1:36:CYS:C	1:37:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	PFX	2-[2-(2-azanylethoxy)ethoxy]ethanoic acid	Assigned chemical shifts, Coordinates
A	21	NLE	NORLEUCINE	Assigned chemical shifts, Distance restraints, Coordinates
A	36	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

0--------10--------20--------30------
XRSCIDTIPKSRCTAFQCKHSXKYRLSFCRKTCGTCX
|||||||||||||||||||||||||||||||||||||
XRSCIDTIPKSRCTAFQCKHSXKYRLSFCRKTCGTCX
--------10--------20--------30-------

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_15983_2k9e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	7		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	314		100.0 (chain: A, length: 37)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3 (1)	undefined	16.2 (chain: A, length: 37)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	914 (1)	noe	94.6 (chain: A, length: 37)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	14 (1)	hbond	37.8 (chain: A, length: 37)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%

0--------10--------20--------30------
XRSCIDTIPKSRCTAFQCKHSXKYRLSFCRKTCGTCX
|||||||||||||||||||||||||||||||||||||
XRSCIDTIPKSRCTAFQCKHSXKYRLSFCRKTCGTCX

Total number of assignments
- ¹H chemical shifts: 246
- ¹³C chemical shifts: 35
- ¹⁵N chemical shifts: 33

Completeness of assignments

Entity_assemble_ID: A

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
0	PFX

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	LYS	HZ1	7.34
9	LYS	HZ2	7.34
9	LYS	HZ3	7.34
11	ARG	HH11	7.24
11	ARG	HH12	7.24
13	THR	HG1	5.78
19	HIS	HD1	8.34
21	NLE	N	132.41
22	LYS	HZ1	7.48
22	LYS	HZ2	7.48
22	LYS	HZ3	7.48
24	ARG	HH11	6.52
24	ARG	HH12	6.52
24	ARG	HH21	6.77
24	ARG	HH22	6.77
29	ARG	HH11	6.65
29	ARG	HH12	6.65
29	ARG	HH21	7.21
29	ARG	HH22	7.21
30	LYS	HZ1	7.49
30	LYS	HZ2	7.49
30	LYS	HZ3	7.49

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	221	218	98.6
¹³C chemical shifts	154	34	22.1
¹⁵N chemical shifts	39	32	82.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	68	97.1
¹³C chemical shifts	69	34	49.3
¹⁵N chemical shifts	34	32	94.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	150	99.3
¹³C chemical shifts	85	0	0.0
¹⁵N chemical shifts	5	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	11	91.7
¹³C chemical shifts	12	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0
¹³C chemical shifts	16	0	0.0

Redox state of CYS
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: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 16.2%
- Total number of restraints: 3
- Weight of restraints: 1.0 (3)
- Potential type of restraints: square-well-parabolic (3)
- Range of distance target values: 2.02, 2.02 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 94.6%
  - Total number of restraints: 910
  - Weight of restraints: 1.0 (910)
  - Potential type of restraints: square-well-parabolic (910)
  - Range of distance target values: 2.15, 4.66 (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_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 37.8%
    - Total number of restraints: 14
    - Weight of restraints: 1.0 (14)
    - Potential type of restraints: square-well-parabolic (14)
    - Range of distance target values: 2.1, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

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Found 1 Document (0.759 seconds)

BMRB: 15983

Sample #1

Sample #2

Related entities 1. ShK-192, : 1 : 11 : 17 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail