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Found 1 Document (0.669 seconds)

BMRB: 18684

2LXO

Identification of the Structural Traits Mediating the Antimicrobial Activity of a Chimeric Peptide of HBD2 and HBD3

Authors

Spudy, B., Soennichsen, F.D., Waetzig, G.H., Groetzinger, J., Jung, S.

Assembly

Chimeric Peptide of HBD2 and HBD3

Entity

1. Chimeric Peptide of HBD2 and HBD3 (polymer), 44 monomers, 4971.982 Da Detail

GIINTLQKYY CRVRGAICHP VFCPRRYKQI GTCGLPGTKC CKKP

Formula weight

4971.982 Da

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 68.2 %, Completeness: 50.2 %, Completeness (bb): 62.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	50.2 % (141 of 281)	50.2 % (141 of 281)
Backbone	62.9 % (56 of 89)	62.9 % (56 of 89)
Sidechain	44.3 % (85 of 192)	44.3 % (85 of 192)
Aromatic	52.6 % (10 of 19)	52.6 % (10 of 19)
Methyl	25.0 % (5 of 20)	25.0 % (5 of 20)

1. entity

GIINTLQKYY CRVRGAICHP VFCPRRYKQI GTCGLPGTKC CKKP

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 4.6

#	Name	Isotope labeling	Concentration
1	HBD2_HBD3	natural abundance	0.15 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

Protein Blocks Logo

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

Release date

2013-08-11

Citation

Identification of structural traits that increase the antimicrobial activity of a chimeric peptide of human β-defensins 2 and 3
Spudy, B., Soennichsen, F.D., Waetzig, G.H., Groetzinger, J., Jung, S.
Biochem. Biophys. Res. Commun. (2012), 427, 207-211, PubMed 22995312 , DOI 10.1016/j.bbrc.2012.09.052 , Abstract

Related entities 1. Chimeric Peptide of HBD2 and HBD3, : 1 : 27 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18684_2lxo.nef
Input source #2: Coordindates	2lxo.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:11:CYS:SG	A:40:CYS:SG	unknown	unknown	2.141
A:18:CYS:SG	A:33:CYS:SG	unknown	unknown	2.155

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--------20--------30--------40----
GIINTLQKYYCRVRGAICHPVFCPRRYKQIGTCGLPGTKCCKKP
||||||||||||||||||||||||||||||||||||||||||||
GIINTLQKYYCRVRGAICHPVFCPRRYKQIGTCGLPGTKCCKKP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_18684_2lxo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	134		65.9 (chain: A, length: 44)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	547 (1)	noe	70.5 (chain: A, length: 44)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	9 (1)	undefined	13.6 (chain: A, length: 44)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	147 (1)	noe	56.8 (chain: A, length: 44)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	12 (1)	hbond	22.7 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 65.9%
- Total number of assignments
  - ¹H chemical shifts: 134
- 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)
19	HIS	HE2	7.878

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	281	133	47.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	56	62.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	77	40.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	5	25.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	10	52.6

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 70.5%
- Total number of restraints: 547
- Weight of restraints: 1.0 (547)
- Potential type of restraints: upper-bound-parabolic (547)
- Range of distance target values: 0.05, 6.0 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 13.6%
  - Total number of restraints: 9
  - Weight of restraints: 1.0 (9)
  - Potential type of restraints: upper-bound-parabolic (9)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_5
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 56.8%
    - Total number of restraints: 147
    - Weight of restraints: 1.0 (147)
    - Potential type of restraints: lower-bound-parabolic (147)
    - Range of distance target values: 0.05, 0.05 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_4
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 22.7%
      - Total number of restraints: 12
        Total hydrogen bond restraints: 12
        O...H-x (too close!): 3
        O...h-N (too close!): 3
        Long range: 6
        O...H-x (too close!): 3
        O...h-N (too close!): 3
      - Weight of restraints: 1.0 (12)
        Total hydrogen bond restraints: 1.0 (12)
        O...H-x (too close!): 1.0 (3)
        O...h-N (too close!): 1.0 (3)
        Long range: 1.0 (6)
        O...H-x (too close!): 1.0 (3)
        O...h-N (too close!): 1.0 (3)
      - Potential type of restraints: upper-bound-parabolic (12)
        Total hydrogen bond restraints: upper-bound-parabolic (12)
        O...H-x (too close!): upper-bound-parabolic (3)
        O...h-N (too close!): upper-bound-parabolic (3)
        Long range: upper-bound-parabolic (6)
        O...H-x (too close!): upper-bound-parabolic (3)
        O...h-N (too close!): upper-bound-parabolic (3)
      - Range of distance target values: 1.8, 2.7 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map

Keywords antimicrobial peptide, designer peptide

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Found 1 Document (0.669 seconds)

BMRB: 18684

Sample

Related entities 1. Chimeric Peptide of HBD2 and HBD3, : 1 : 27 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail