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Found 1 Document (0.416 seconds)

BMRB: 30176

5TBG

The Solution Structure of the Magnesium-bound Conantokin-R1B Mutant

Authors

Castellino, F.J., Yuan, Y.

Assembly

Conantokin

Entity

1. Conantokin (polymer, Thiol state: not present), 20 monomers, 2384.356 Da Detail

GEXXLAXKAP XFARXLANYX

Formula weight

2384.356 Da

Source organism

Conus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 70.0 %, Completeness: 77.8 %, Completeness (bb): 75.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.8 % (126 of 162)	82.1 % (69 of 84)	70.3 % (45 of 64)	85.7 % (12 of 14)
Backbone	75.6 % (62 of 82)	89.3 % (25 of 28)	63.4 % (26 of 41)	84.6 % (11 of 13)
Sidechain	82.8 % (77 of 93)	78.6 % (44 of 56)	88.9 % (32 of 36)	100.0 % (1 of 1)
Aromatic	55.6 % (10 of 18)	55.6 % (5 of 9)	55.6 % (5 of 9)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

1. entity 1

GEXXLAXKAP XFARXLANYX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 7.0, Details 20 mM [U-2H] HEPES, 20 mM Mg2+, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1		0.0 ~ 0.0 mM
2	HEPES	[U-2H]	20 mM
3	Mg2+	natural abundance	20 mM

Protein Blocks Logo

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

Release date

2017-05-11

Citation

Discerning the Role of the Hydroxyproline Residue in the Structure of Conantokin Rl-B and Its Role in GluN2B Subunit-Selective Antagonistic Activity toward N-Methyl-d-Aspartate Receptors
Yuan, Y., Balsara, R.D., Zajicek, J., Kunda, S., Castellino, F.J.
Biochemistry (2016), 55, 7112-7122, PubMed 27981829 , DOI 10.1021/acs.biochem.6b00962 , Abstract

Related entities 1. Conantokin, : 1 : 2 : 1 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30176_5tbg.nef
Input source #2: Coordindates	5tbg.cif
Diamagnetism of the molecular assembly	True (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:GLU:C	1:3:CGU:N	unknown	unknown	n/a
1:3:CGU:C	1:4:CGU:N	unknown	unknown	n/a
1:4:CGU:C	1:5:LEU:N	unknown	unknown	n/a
1:6:ALA:C	1:7:CGU:N	unknown	unknown	n/a
1:7:CGU:C	1:8:LYS:N	unknown	unknown	n/a
1:10:PRO:C	1:11:CGU:N	unknown	unknown	n/a
1:11:CGU:C	1:12:PHE:N	unknown	unknown	n/a
1:14:ARG:C	1:15:CGU:N	unknown	unknown	n/a
1:15:CGU:C	1:16:LEU:N	unknown	unknown	n/a
1:19:TYR:C	1:20:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Torsion angle restraints, Coordinates
A	4	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	7	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	11	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	15	CGU	GAMMA-CARBOXY-GLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	20	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20
GEXXLAXKAPXFARXLANYX
||||||||||||||||||||
GEXXLAXKAPXFARXLANYX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	20	0	0	100.0

Content subtype: combined_30176_5tbg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	10		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	178		100.0 (chain: A, length: 20)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	158 (1)	noe	90.0 (chain: A, length: 20)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	7 (1)	hbond	40.0 (chain: A, length: 20)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	28 (28)	.	90.0 (chain: A, length: 20)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 100
  - ¹³C chemical shifts: 60
  - ¹⁵N chemical shifts: 18
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Comp_index_ID	Comp_ID
3	CGU
4	CGU
7	CGU
11	CGU
15	CGU

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	76	88.4
¹³C chemical shifts	64	45	70.3
¹⁵N chemical shifts	16	13	81.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	27	96.4
¹³C chemical shifts	28	13	46.4
¹⁵N chemical shifts	14	12	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	49	84.5
¹³C chemical shifts	36	32	88.9
¹⁵N chemical shifts	2	1	50.0

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	5	55.6
¹³C chemical shifts	9	5	55.6

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 90.0%
- Total number of restraints: 158
- Weight of restraints: 1.0 (158)
- Potential type of restraints: square-well-parabolic (158)
- Range of distance target values: 2.5, 5.0 (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: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 40.0%
  - Total number of restraints: 7
  - Weight of restraints: 1.0 (7)
  - Potential type of restraints: square-well-parabolic (7)
  - Range of distance target values: 1.9, 2.85 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 90.0%
- Total number of restraints: 28
- Total number of restraints per polymer type: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: square-well-parabolic (28)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TRANSPORT PROTEIN INHIBITOR

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Found 1 Document (0.416 seconds)

BMRB: 30176

Sample

Related entities 1. Conantokin, : 1 : 2 : 1 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail