BMRBj - BMREntryMaster

Found 1 Document (1.295 seconds)

BMRB: 30332

6AMW

Abl1b Regulatory Module 'Activating' conformation

Authors

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

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: 80.8 %, Completeness: 74.5 %, Completeness (bb): 79.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.5 % (2175 of 2921)	72.4 % (1101 of 1521)	77.5 % (877 of 1131)	73.2 % (197 of 269)
Backbone	79.2 % (1187 of 1498)	78.7 % (407 of 517)	79.2 % (588 of 742)	80.3 % (192 of 239)
Sidechain	69.9 % (1157 of 1655)	68.4 % (687 of 1004)	74.9 % (465 of 621)	16.7 % (5 of 30)
Aromatic	68.6 % (188 of 274)	68.6 % (94 of 137)	68.9 % (91 of 132)	60.0 % (3 of 5)
Methyl	79.8 % (190 of 238)	78.2 % (93 of 119)	81.5 % (97 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, Details 0.3 mM [U-99% 13C; U-99% 15N] Abl1b, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 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: -0.1 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: -0.1 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: 0.0 ppm, Outliers: 1 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: 0.24 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2017-08-27

Citation

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

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 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.3 mM [U-99% 13C; U-99% 15N] Abl1b, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 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 2D 1H-13C 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 %

3 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 %

4 3D HN(COCA)CB

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 %

5 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 %

6 3D HNCA

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 %

7 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 %

8 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 %

9 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 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30332_6amw.nef
Input source #2: Coordindates	6amw.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_30332_6amw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2079		75.7 (chain: A, length: 255)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4592 (1)	noe	72.9 (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	416 (416)	.	69.4 (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: 75.7%
- Total number of assignments
  - ¹H chemical shifts: 1065
  - ¹³C chemical shifts: 834
  - ¹⁵N chemical shifts: 180
- 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	1065	70.0
¹³C chemical shifts	1131	834	73.7
¹⁵N chemical shifts	284	180	63.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	517	387	74.9
¹³C chemical shifts	510	382	74.9
¹⁵N chemical shifts	239	177	74.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1004	678	67.5
¹³C chemical shifts	621	452	72.8
¹⁵N chemical shifts	45	3	6.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	120	96	80.0
¹³C chemical shifts	120	96	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	94	68.6
¹³C chemical shifts	132	91	68.9
¹⁵N chemical shifts	5	3	60.0

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: 72.9%
- Total number of restraints: 4592
- Weight of restraints: 1.0 (4592)
- Potential type of restraints: square-well-parabolic (4592)
- Range of distance target values: 2.25, 4.93 (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: 1.9, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 255, Sequence coverage: 69.4%
- Total number of restraints: 416
- Total number of restraints per polymer type: 416
- Weight of restraints: 1.0 (416)
- Potential type of restraints: square-well-parabolic (416)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SIGNALING PROTEIN, Signaling protein kinase

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Found 1 Document (1.295 seconds)

BMRB: 30332

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

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 9 experiments Detail

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NMR combined restraints 5 contents Detail