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Found 1 Document (0.545 seconds)

BMRB: 34215

6F7O

NMR structure of an Odin-Sam1 stapled peptide

Authors

Leone, M., Mercurio, F.A.

Assembly

Ephrin type-A receptor 2 (E.C.2.7.10.1)

Entity

1. Ephrin type-A receptor 2 (E.C.2.7.10.1) (polymer, Thiol state: not present), 15 monomers, 1597.883 Da Detail

XDPQHXRKLX QAARX

Formula weight

1597.883 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 73.3 %, Completeness: 90.5 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	90.5 % (67 of 74)	90.5 % (67 of 74)
Backbone	100.0 % (21 of 21)	100.0 % (21 of 21)
Sidechain	86.8 % (46 of 53)	86.8 % (46 of 53)
Aromatic	50.0 % (1 of 2)	50.0 % (1 of 2)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. entity 1

XDPQHXRKLX QAARX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 930 uM A5ST, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	A5ST	natural abundance		930 uM

Release date

2017-12-21

Citation

Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2
Mercurio, F.A., Pirone, L., Di Natale, C., Marasco, D., Pedone, E.M., Leone, M.
Bioorg. Chem. (2018), 80, 602-610, PubMed 30036816 , DOI 10.1016/j.bioorg.2018.07.013 , Abstract

Related entities 1. Ephrin type-A receptor 2 (E.C.2.7.10.1), : 1 : 8 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34215_6f7o.nef
Input source #2: Coordindates	6f7o.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
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

None

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:ACE:C	1:2:ASP:N	unknown	unknown	n/a
1:5:HIS:C	1:6:MK8:N	unknown	unknown	n/a
1:6:MK8:C	1:7:ARG:N	unknown	unknown	n/a
1:6:MK8:CE	1:10:MK8:CE	unknown	unknown	n/a
1:9:LEU:C	1:10:MK8:N	unknown	unknown	n/a
1:10:MK8:C	1:11:GLN:N	unknown	unknown	n/a
1:14:ARG:C	1:15:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	ACE	ACETYL GROUP	Assigned chemical shifts, Torsion angle restraints, Coordinates
A	6	MK8	2-methyl-L-norleucine	Assigned chemical shifts, Coordinates
A	10	MK8	2-methyl-L-norleucine	Assigned chemical shifts, Coordinates
A	15	NH2	AMINO GROUP	Torsion angle restraints, Coordinates

Sequence alignments

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

--------10-----
XDPQHXRKLXQAARX
|||||||||||||||
XDPQHXRKLXQAARX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	15	0	0	100.0

Content subtype: combined_34215_6f7o.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_chemical_shifts_1	Warning	84		93.3 (chain: A, length: 15)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	165 (1)	noe	73.3 (chain: A, length: 15)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	47 (46)	.	86.7 (chain: A, length: 15)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 93.3%
- Total number of assignments
  - ¹H chemical shifts: 84
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
5	HIS	HD1	7.05

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	83	86.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	21	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	62	83.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	1	50.0

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: 15, Sequence coverage: 73.3%
- Total number of restraints: 163
- Weight of restraints: 1.0 (163)
- Potential type of restraints: upper-bound-parabolic (163)
- Range of distance target values: 3.05, 7.26 (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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 86.7%
- Total number of restraints: 46
- Total number of restraints per polymer type: 46
- Weight of restraints: 1.0 (46)
- Potential type of restraints: square-well-parabolic (46)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Sam domain, signaling protein, stapled peptide

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Found 1 Document (0.545 seconds)

BMRB: 34215

Sample

Related entities 1. Ephrin type-A receptor 2 (E.C.2.7.10.1), : 1 : 8 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail