BMRBj - BMREntryMaster

Found 1 Document (0.411 seconds)

BMRB: 30311

5W96

Solution structure of phage displayed derived peptide inhibitor of frizzled 7 receptor

Authors

Fu, Y.

Assembly

Frizzled 7 binding peptide

Entity

1. Frizzled 7 binding peptide (polymer, Thiol state: not present), 14 monomers, 1754.977 × 2 Da Detail

LPSDDLEFWC HVMY

Total weight

3509.954 Da

Max. entity weight

1754.977 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.9 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	90.9 % (80 of 88)	90.9 % (80 of 88)
Backbone	96.3 % (26 of 27)	96.3 % (26 of 27)
Sidechain	88.5 % (54 of 61)	88.5 % (54 of 61)
Aromatic	88.2 % (15 of 17)	88.2 % (15 of 17)
Methyl	83.3 % (5 of 6)	83.3 % (5 of 6)

1. Fz7 binding peptide

LPSDDLEFWC HVMY

Show sample condition

Sample

Solvent system 90%H2O 10%acetonitrile, Pressure 1 atm, Temperature 298 K, pH 7.3, Details 1 mM Fz binding peptide, 10 mM sodium phosphate, 10 % acentonitrile, 90%H2O 10%acetonitrile

#	Name	Isotope labeling	Concentration
1	Fz binding peptide	natural abundance	1 mM
2	acentonitrile	natural abundance	10 %
3	sodium phosphate	natural abundance	10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5W96, Strand ID: A, B Detail

Release date

2017-07-09

Citation

A selective peptide inhibitor of Frizzled 7 receptors disrupts intestinal stem cells
Nile, A.H., de Sousa E Melo, F., Mukund, S., Piskol, R., Hansen, S., Zhou, L., Zhang, Y., Fu, Y., Gogol, E.B., Komuves, L.G., Modrusan, Z., Angers, S., Franke, Y., Koth, C., Fairbrother, W.J., Wang, W., de Sauvage, F.J., Hannoush, R.N.
Nat. Chem. Biol. (2018), 14, 582-590, PubMed 29632413 , DOI 10.1038/s41589-018-0035-2 , Abstract

Related entities 1. Frizzled 7 binding peptide, : 1 : 1 : 1 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30311_5w96.nef
Input source #2: Coordindates	5w96.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:10:CYS:SG	B:60:CYS:SG	unknown	unknown	2.03

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----
LPSDDLEFWCHVMY
||||||||||||||
LPSDDLEFWCHVMY

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

--------60----
LPSDDLEFWCHVMY
||||||||||||||
LPSDDLEFWCHVMY
--------10----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	14	0	0	100.0
B	B	14	0	0	100.0

Content subtype: combined_30311_5w96.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	166		100.0 (chain: A, length: 14), 100.0 (chain: B, length: 14)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	463 (1)	noe	100.0 (chain: A, length: 14), 100.0 (chain: B, length: 14)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 14, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 14, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 166
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	79	89.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	26	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	53	86.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	15	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	79	89.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	26	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	53	86.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	15	88.2

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 14, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 14, Sequence coverage: 100.0%
- Total number of restraints: 461
- Weight of restraints: 1.0 (461)
- Potential type of restraints: square-well-parabolic (461)
- Range of distance target values: 1.51, 3.3 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords peptide inhibitor

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Found 1 Document (0.411 seconds)

BMRB: 30311

Sample

Related entities 1. Frizzled 7 binding peptide, : 1 : 1 : 1 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail