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Found 1 Document (0.407 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

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

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Found 1 Document (0.407 seconds)

BMRB: 18875

Sample #1

Sample #2

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