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Found 1 Document (1.197 seconds)

BMRB: 30331

6AMV

Abl 1b Regulatory Module 'inhibiting state'

Authors

Kalodimos, C.G., Saleh, T., Rossi, P.

Assembly

Tyrosine-protein kinase ABL1 (E.C.2.7.10.2)

Entity

1. Tyrosine-protein kinase ABL1 (E.C.2.7.10.2) (polymer, Thiol state: not present), 255 monomers, 28311.02 Da Detail

MGQQPGKVLG DQRRPSLPAL HFIKGAGKRE SSRHGGPHCN VFVEHEALQR PVASDFEPQG LSEAARWNSK ENLLAGPSEN DPNLFVALYD FVASGDNTLS ITKGEKLRVL GYNHNGEWAE AQTKNGQGWV PSNYITPVNS LEKHSWYHGP VSRNAAEYLL SSGINGSFLV RESESSPGQR SISLRYEGRV YHYRINTASD GKLYVSSESR FNTLAELVHH HSTVADGLIT TLHYPAPKRN KPTVYGVSPN YDKWE

Formula weight

28311.02 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 61.8 %, Completeness (bb): 79.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.8 % (1804 of 2921)	44.9 % (683 of 1521)	78.9 % (892 of 1131)	85.1 % (229 of 269)
Backbone	79.6 % (1192 of 1498)	57.4 % (297 of 517)	90.7 % (673 of 742)	92.9 % (222 of 239)
Sidechain	50.0 % (828 of 1655)	38.4 % (386 of 1004)	70.0 % (435 of 621)	23.3 % (7 of 30)
Aromatic	73.0 % (200 of 274)	73.0 % (100 of 137)	72.0 % (95 of 132)	100.0 % (5 of 5)
Methyl	81.5 % (194 of 238)	82.4 % (98 of 119)	80.7 % (96 of 119)

1. Tyrosine-protein kinase ABL1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM [U-99% 13C; U-99% 15N] Abl1b, 20 mM potassium phosphate, 5 mM beta-mercaptoethanol, 100 mM potassium chloride, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6AMV, Strand ID: A Detail

Release date

2017-08-27

Citation

Atomic view of the energy landscape in the allosteric regulation of Abl kinase
Saleh, T., Rossi, P., Kalodimos, C.G.
Nat. Struct. Mol. Biol. (2017), 24, 893-901, PubMed 28945248 , DOI 10.1038/nsmb.3470 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30332 released on 2017-08-27
Title Abl1b Regulatory Module 'Activating' conformation

Related entities 1. Tyrosine-protein kinase ABL1 (E.C.2.7.10.2), : 1 : 1 : 3 : 18 entities Detail

Interaction partners 1. Tyrosine-protein kinase ABL1 (E.C.2.7.10.2), : 18 interactors Detail

More details for 18 interactors identified by 13 citations

Experiments performed 8 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM [U-99% 13C; U-99% 15N] Abl1b, 20 mM potassium phosphate, 5 mM beta-mercaptoethanol, 100 mM potassium chloride, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

2 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

4 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

6 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

7 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

8 3D HNCO

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Abl1b	[U-99% 13C; U-99% 15N]	0.3 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	sodium azide	natural abundance	0.05 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30331_6amv.nef
Input source #2: Coordindates	6amv.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MGQQPGKVLGDQRRPSLPALHFIKGAGKRESSRHGGPHCNVFVEHEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGQQPGKVLGDQRRPSLPALHFIKGAGKRESSRHGGPHCNVFVEHEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLS

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
ITKGEKLRVLGYNHNGEWAEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ITKGEKLRVLGYNHNGEWAEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASD

-------210-------220-------230-------240-------250-----
GKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
GKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	255	0	0	100.0

Content subtype: combined_30331_6amv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1695		94.5 (chain: A, length: 255)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1372 (1)	noe	63.5 (chain: A, length: 255)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	124 (1)	hbond	31.4 (chain: A, length: 255)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	331 (331)	.	73.7 (chain: A, length: 255)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 255, Sequence coverage: 94.5%
- Total number of assignments
  - ¹H chemical shifts: 602
  - ¹³C chemical shifts: 869
  - ¹⁵N chemical shifts: 224
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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	1521	602	39.6
¹³C chemical shifts	1131	869	76.8
¹⁵N chemical shifts	284	224	78.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	517	274	53.0
¹³C chemical shifts	510	451	88.4
¹⁵N chemical shifts	239	219	91.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1004	328	32.7
¹³C chemical shifts	621	418	67.3
¹⁵N chemical shifts	45	5	11.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	120	95	79.2
¹³C chemical shifts	120	95	79.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	100	73.0
¹³C chemical shifts	132	95	72.0
¹⁵N chemical shifts	5	5	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 255, Sequence coverage: 63.5%
- Total number of restraints: 1372
- Weight of restraints: 1.0 (1372)
- Potential type of restraints: square-well-parabolic (1372)
- Range of distance target values: 2.34, 5.1 (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: 255, Sequence coverage: 31.4%
  - Total number of restraints: 124
  - Weight of restraints: 1.0 (124)
  - Potential type of restraints: square-well-parabolic (124)
  - Range of distance target values: 1.98, 2.96 (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: 255, Sequence coverage: 73.7%
- Total number of restraints: 331
- Total number of restraints per polymer type: 331
- Weight of restraints: 1.0 (331)
- Potential type of restraints: square-well-parabolic (331)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SIGNALING PROTEIN

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Found 1 Document (1.197 seconds)

BMRB: 30331

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Tyrosine-protein kinase ABL1 (E.C.2.7.10.2), : 1 : 1 : 3 : 18 entities Detail

Interaction partners 1. Tyrosine-protein kinase ABL1 (E.C.2.7.10.2), : 18 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail