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Found 1 Document (0.581 seconds)

BMRB: 25928

2NA5

NMR solution structure of vitamin B12 conjugates of PYY3-36

Authors

Doyle, R.P., Henry, K.E., Roth, C.L., Kerwood, D.J., Allis, D.G., Holz, G.G., Zubieta, J.

Assembly

vitamin B12 conjugate of PYY3-36

Entity

1. vitamin B12 conjugate of PYY3-36 (polymer, Thiol state: not present), 35 monomers, 4267.653 Da Detail

IXPEAPGEDA SPEELNRYYA SLRHYLNLVV TRQRY

Formula weight

4267.653 Da

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 90.1 %, Completeness (bb): 93.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	90.1 % (191 of 212)	90.1 % (191 of 212)
Backbone	93.9 % (62 of 66)	93.9 % (62 of 66)
Sidechain	88.4 % (129 of 146)	88.4 % (129 of 146)
Aromatic	55.6 % (10 of 18)	55.6 % (10 of 18)
Methyl	72.2 % (13 of 18)	72.2 % (13 of 18)

1. vitamin B12 conjugate of PYY3-36

IXPEAPGEDA SPEELNRYYA SLRHYLNLVV TRQRY

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Temperature 273 K, pH 5.5 (±.1), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	vitamin B12 conjugate of PYY3-36	natural abundance	1 (±0.2) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 1 models in PDB: 2NA5, Strand ID: A Detail

Release date

2016-09-14

Citation

Solution Structure and Constrained Molecular Dynamics Study of Vitamin B12 Conjugates of the Anorectic Peptide PYY(3-36)
Henry, K.E., Kerwood, D.J., Allis, D.G., Workinger, J.L., Bonaccorso, R.L., Holz, G.G., Roth, C.L., Zubieta, J.A., Doyle, R.P.
ChemMedChem (2016), 11, 1015-1021, PubMed 27027248 , DOI 10.1002/cmdc.201600073 , Abstract

Related entities 1. vitamin B12 conjugate of PYY3-36, : 1 : 117 entities Detail

Interaction partners 1. vitamin B12 conjugate of PYY3-36, : 5 interactors Detail

More details for 5 interactors identified by 2 citations

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25928_2na5.nef
Input source #2: Coordindates	2na5.cif
Diamagnetism of the molecular assembly	False (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)
1:2:4QK:C	1:3:PRO:N	unknown	unknown	n/a
1:2:4QK:NZ2	2:1:CNC:C5R	unknown	unknown	n/a
1:1:ILE:C	1:2:4QK:N	unknown	unknown	n/a
2:1:CNC:N3B	2:1:CNC:CO	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	5	.	Not matched with CCD	None
A	4	4QK	6-[4-(2-aminoethyl)-1H-1,2,3-triazol-1-yl]-L-norleucine	None
B	1	CNC	CYANOCOBALAMIN	None

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	1	0	100.0

Content subtype: combined_25928_2na5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	190		91.4 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	93 (1)	noe	82.9 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 91.4%
- Total number of assignments
  - ¹H chemical shifts: 190
- 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
4	4QK

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	207	190	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	62	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	143	128	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	12	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	10	55.6

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 82.9%
- Total number of restraints: 93
- Weight of restraints: 1.0 (93)
- Potential type of restraints: upper-bound-parabolic (93)
- Range of distance target values: 1.8, 1.8 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords helix, vitamin-peptide conjugate

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Found 1 Document (0.581 seconds)

BMRB: 25928

Sample

Related entities 1. vitamin B12 conjugate of PYY3-36, : 1 : 117 entities Detail

Interaction partners 1. vitamin B12 conjugate of PYY3-36, : 5 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail