BMRBj - BMREntryMaster

Found 1 Document (0.665 seconds)

BMRB: 34213

6F7M

NMR structure of EphA2-Sam stapled peptides (S13ST)

Authors

Mercurio, F.A., Leone, M.

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), 27 monomers, 2898.476 Da Detail

XKRIGVRLPG HQKRXAYSXL GLKDQVX

Formula weight

2898.476 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 85.2 %, Completeness: 97.4 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	97.4 % (148 of 152)	97.4 % (148 of 152)
Backbone	100.0 % (48 of 48)	100.0 % (48 of 48)
Sidechain	96.2 % (100 of 104)	96.2 % (100 of 104)
Aromatic	83.3 % (5 of 6)	83.3 % (5 of 6)
Methyl	100.0 % (13 of 13)	100.0 % (13 of 13)

1. entity 1

XKRIGVRLPG HQKRXAYSXL GLKDQVX

Show sample condition

Sample

Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 K, pH 7.1, Details 650 uM S13ST, trifluoroethanol/water

#	Name	Isotope labeling	Type	Concentration
1	S13ST	natural abundance		650 uM

Release date

2018-07-22

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 : 11 : 17 entities Detail

Interaction partners 1. Ephrin type-A receptor 2 (E.C.2.7.10.1), : 3 interactors Detail

More details for 3 interactors identified by 3 citations

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_34213_6f7m.nef
Input source #2: Coordindates	6f7m.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:LYS:N	unknown	unknown	n/a
1:14:ARG:C	1:15:MK8:N	unknown	unknown	n/a
1:15:MK8:C	1:16:ALA:N	unknown	unknown	n/a
1:15:MK8:CE	1:19:MK8:CE	unknown	unknown	n/a
1:18:SER:C	1:19:MK8:N	unknown	unknown	n/a
1:19:MK8:C	1:20:LEU:N	unknown	unknown	n/a
1:26:VAL:C	1:27: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	15	MK8	2-methyl-L-norleucine	Assigned chemical shifts, Coordinates
A	19	MK8	2-methyl-L-norleucine	Assigned chemical shifts, Coordinates
A	27	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-------
XKRIGVRLPGHQKRXAYSXLGLKDQVX
|||||||||||||||||||||||||||
XKRIGVRLPGHQKRXAYSXLGLKDQVX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_34213_6f7m.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	167		100.0 (chain: A, length: 27)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	187 (1)	noe	74.1 (chain: A, length: 27)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	108 (104)	.	92.6 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 167
- 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)
11	HIS	HD1	7.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	174	166	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	48	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	125	118	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	5	83.3

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: 27, Sequence coverage: 74.1%
- Total number of restraints: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: upper-bound-parabolic (186)
- Range of distance target values: 3.02, 7.6 (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: 27, Sequence coverage: 92.6%
- Total number of restraints: 104
- Total number of restraints per polymer type: 104
- Weight of restraints: 1.0 (104)
- Potential type of restraints: square-well-parabolic (104)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ephrin receptor, Sam domain, signaling protein, stapled peptide

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.665 seconds)

BMRB: 34213

Sample

Related entities 1. Ephrin type-A receptor 2 (E.C.2.7.10.1), : 1 : 11 : 17 entities Detail

Interaction partners 1. Ephrin type-A receptor 2 (E.C.2.7.10.1), : 3 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail