BMRBj - BMREntryMaster

Found 1 Document (0.46 seconds)

BMRB: 18875

2M1P

[Aba5,14]BTD-2

Authors

Conibear, A.C., Rosengren, K., Daly, N.L., Troiera Henriques, S., Craik, D.J.

Assembly

[Aba5,14]BTD-2, cyclic peptide

Entity

1. [Aba5,14]BTD-2, cyclic peptide (polymer, Thiol state: all disulfide bound), 18 monomers, 2048.537 Da Detail

GVCRXVCRRG VCRXVCRR

Formula weight

2048.537 Da

Entity Connection

peptide 1, disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS16:SG
2	disulfide	sing	1:CYS7:SG	1:CYS12:SG
3	peptide	sing	1:GLY1:N	1:ARG18:C

Source organism

Papio anubis

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.9 %, Completeness: 90.7 %, Completeness (bb): 81.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	90.7 % (147 of 162)	100.0 % (96 of 96)	77.3 % (51 of 66)
Backbone	81.3 % (65 of 80)	100.0 % (34 of 34)	67.4 % (31 of 46)
Sidechain	100.0 % (96 of 96)	100.0 % (62 of 62)	100.0 % (34 of 34)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

1. [Aba5,14]BTD-2

GVCRXVCRRG VCRXVCRR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 0.6 mM, pH 4

#	Name	Isotope labeling	Concentration
1	[Aba5,14]BTD-2	natural abundance	0.6 mM
2	DSS	natural abundance	10 ug
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4, Details 0.6 mM, pH 4

#	Name	Isotope labeling	Concentration
5	[Aba5,14]BTD-2	natural abundance	0.6 mM
6	DSS	natural abundance	10 ug
7	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M1P, Strand ID: A Detail

Release date

2013-02-26

Citation

The cyclic cystine ladder in θ-defensins is important for structure and stability, but not antibacterial activity
Conibear, A.C., Rosengren, K., Daly, N.L., Henriques, S., Craik, D.J.
J. Biol. Chem. (2013), 288, 10830-10840, PubMed 23430740 , DOI 10.1074/jbc.M113.451047 , Abstract

Entries sharing articles BMRB: 5 entries Detail

  BMRB: 18913 released on 2013-02-26
    Title [Aba3,16]BTD-2
  BMRB: 18914 released on 2013-02-26
    Title [Aba3,7,12,16]BTD-2
  BMRB: 18931 released on 2013-02-26
    Title [Aba5,7,12,14]BTD-2
  BMRB: 18937 released on 2013-02-26
    Title [Aba3,5,7,12,14,16]BTD-2
  BMRB: 18938 released on 2013-02-26
    Title BTD-2[3,4]

Related entities 1. [Aba5,14]BTD-2, cyclic peptide, : 1 : 2 : 5 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18875_2m1p.nef
Input source #2: Coordindates	2m1p.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	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	True (see coordinates for details)
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:3:CYS:SG	A:16:CYS:SG	oxidized, CA 55.307, CB 46.464 ppm	oxidized, CA 55.198, CB 47.739 ppm	2.047
A:7:CYS:SG	A:12:CYS:SG	oxidized, CA 55.198, CB 47.739 ppm	oxidized, CA 55.307, CB 46.464 ppm	2.033

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)
1:4:ARG:C	1:5:ABA:N	unknown	unknown	n/a
1:5:ABA:C	1:6:VAL:N	unknown	unknown	n/a
1:13:ARG:C	1:14:ABA:N	unknown	unknown	n/a
1:14:ABA:C	1:15:VAL:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	5	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	14	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------
GVCRXVCRRGVCRXVCRR
||||||||||||||||||
GVCRXVCRRGVCRXVCRR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0

Content subtype: combined_18875_2m1p.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_chem_shift_list_1	Warning	164		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	143 (1)	noe	94.4 (chain: A, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	16 (1)	hbond	44.4 (chain: A, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	41 (41)	.	100.0 (chain: A, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 110
  - ¹³C chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	106	102	96.2
¹³C chemical shifts	72	54	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	36	94.7
¹³C chemical shifts	34	18	52.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	66	97.1
¹³C chemical shifts	38	36	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	8	80.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 94.4%
- Total number of restraints: 143
- Weight of restraints: 1.0 (143)
- Potential type of restraints: square-well-parabolic (143)
- Range of distance target values: 2.1, 4.7 (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: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 44.4%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: square-well-parabolic (16)
  - Range of distance target values: 1.9, 2.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 41
- Total number of restraints per polymer type: 41
- Weight of restraints: 1.0 (41)
- Potential type of restraints: square-well-parabolic (41)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cyclic cystine ladder, cyclic peptides, disulfide bond, theta-defensin

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 (0.46 seconds)

BMRB: 18875

Sample #1

Sample #2

Entries sharing articles BMRB: 5 entries Detail

Related entities 1. [Aba5,14]BTD-2, cyclic peptide, : 1 : 2 : 5 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail