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Found 1 Document (0.428 seconds)

BMRB: 15218

2JP5

1H and 13C Chemical shifts for the ATWLPPR peptide.

Authors

Herve du Penhoat, C.L.M., Badache, S., Bouchemal, N.C.

Assembly

ATWLPPR heptapeptide

Entity

1. ATWLPPR heptapeptide (polymer, Thiol state: not present), 7 monomers, 839.9794 Da Detail

ATWLPPR

Formula weight

839.9794 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.7 %, Completeness (bb): 66.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	86.7 % (72 of 83)	95.7 % (45 of 47)	75.0 % (27 of 36)
Backbone	66.7 % (22 of 33)	83.3 % (10 of 12)	57.1 % (12 of 21)
Sidechain	98.2 % (56 of 57)	100.0 % (35 of 35)	95.5 % (21 of 22)
Aromatic	100.0 % (11 of 11)	100.0 % (6 of 6)	100.0 % (5 of 5)
Methyl	100.0 % (8 of 8)	100.0 % (4 of 4)	100.0 % (4 of 4)

1. ATWLPPR

ATWLPPR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3 at pH 7.0

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3

#	Name	Isotope labeling	Concentration
6	ATWLPPR	natural abundance	6 mM
7	phosphate buffer	natural abundance	10 mM
8	NaCl	natural abundance	140 mM
9	EDTA	natural abundance	5 uM
10	NaN3	natural abundance	2 uM

Protein Blocks Logo

Calculated from 20 models in PDB: 2JP5, Strand ID: A Detail

Release date

2008-02-19

Citation

Structure-function analysis of the antiangiogenic ATWLPPR peptide inhibiting VEGF(165) binding to neuropilin-1 and molecular dynamics simulations of the ATWLPPR/neuropilin-1 complex
Starzec, A., Vassy, R., Badache, S., Bouchemal, N.C., Herve du Penhoat, C.L.M., Perret, G.Y.
Peptides (2007), 28, 2397-2402, PubMed 17983687 , DOI 10.1016/j.peptides.2007.09.013 , Abstract

Experiments performed 11 experiments Detail

1 2D DQF-COSY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3

#	Name	Isotope labeling	Concentration
6	ATWLPPR	natural abundance	6 mM
7	phosphate buffer	natural abundance	10 mM
8	NaCl	natural abundance	140 mM
9	EDTA	natural abundance	5 uM
10	NaN3	natural abundance	2 uM

2 2D 1H-1H NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ATWLPPR	natural abundance	6 mM
7	phosphate buffer	natural abundance	10 mM
8	NaCl	natural abundance	140 mM
9	EDTA	natural abundance	5 uM
10	NaN3	natural abundance	2 uM

3 2D 1H-13C HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ATWLPPR	natural abundance	6 mM
7	phosphate buffer	natural abundance	10 mM
8	NaCl	natural abundance	140 mM
9	EDTA	natural abundance	5 uM
10	NaN3	natural abundance	2 uM

4 2D 1H-1H NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ATWLPPR	natural abundance	6 mM
7	phosphate buffer	natural abundance	10 mM
8	NaCl	natural abundance	140 mM
9	EDTA	natural abundance	5 uM
10	NaN3	natural abundance	2 uM

5 2D 1H-1H NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3 at pH 7.0

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

6 2D 1H-1H COSY

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

7 1D proton spectrum

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

8 1D proton spectrum

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ATWLPPR	natural abundance	6 mM
7	phosphate buffer	natural abundance	10 mM
8	NaCl	natural abundance	140 mM
9	EDTA	natural abundance	5 uM
10	NaN3	natural abundance	2 uM

9 1D proton spectrum

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3 at pH 7.0

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

10 2D 1H-1H TOCSY

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

11 2D 1H-1H NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	ATWLPPR	natural abundance	6 mM
2	phosphate buffer	natural abundance	10 mM
3	NaCl	natural abundance	140 mM
4	EDTA	natural abundance	5 uM
5	NaN3	natural abundance	2 uM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15218_2jp5.nef
Input source #2: Coordindates	2jp5.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

-------
ATWLPPR
|||||||
ATWLPPR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	7	0	0	100.0

Content subtype: combined_15218_2jp5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	72		100.0 (chain: A, length: 7)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	191 (1)	noe	100.0 (chain: A, length: 7)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	25 (25)	.	100.0 (chain: A, length: 7)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 45
  - ¹³C chemical shifts: 27
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	47	45	95.7
¹³C chemical shifts	36	27	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	10	83.3
¹³C chemical shifts	14	6	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	35	100.0
¹³C chemical shifts	22	21	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	5	5	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
- Total number of restraints: 168
- Weight of restraints: 1.0 (168)
- Potential type of restraints: upper-bound-parabolic (168)
- Range of distance target values: 2.02, 7.25 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
- Total number of restraints: 25
- Total number of restraints per polymer type: 25
- Weight of restraints: 1.0 (25)
- Potential type of restraints: square-well-parabolic (25)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords anti-angiogenic peptide, ATWLPPR, binding inhibitor, neuropilin-1, vascular endothelial growth factor-165

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Found 1 Document (0.428 seconds)

BMRB: 15218

Sample #1

Sample #2

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail