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BMRB: 19531

2MET

NMR spatial structure of the trimeric mutant TM domain of VEGFR2 receptor.

Authors

Mineev, K.S., Arseniev, A.A., Shulepko, M., Lyukmanova, E.N., Kirpichnikov, M.P.

Assembly

trimeric mutant TM domain of VEGFR2 receptor

Entity

1. trimeric mutant TM domain of VEGFR2 receptor (polymer, Thiol state: not present), 37 monomers, 4157.014 × 3 Da Detail

EKTNLEIIIL EGTAVIAMFF WLLLVIILRT VKRANGG

Total weight

12471.043 Da

Max. entity weight

4157.014 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.7 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.7 % (440 of 455)	99.6 % (231 of 232)	92.3 % (169 of 183)	100.0 % (40 of 40)
Backbone	97.7 % (217 of 222)	100.0 % (77 of 77)	95.4 % (103 of 108)	100.0 % (37 of 37)
Sidechain	95.9 % (256 of 267)	99.4 % (154 of 155)	90.8 % (99 of 109)	100.0 % (3 of 3)
Aromatic	71.9 % (23 of 32)	100.0 % (16 of 16)	40.0 % (6 of 15)	100.0 % (1 of 1)
Methyl	100.0 % (72 of 72)	100.0 % (36 of 36)	100.0 % (36 of 36)

1. VEGFR-2tm769

EKTNLEIIIL EGTAVIAMFF WLLLVIILRT VKRANGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MET, Strand ID: A, B, C Detail

Release date

2014-07-27

Related entities 1. trimeric mutant TM domain of VEGFR2 receptor, : 1 : 4 : 18 entities Detail

Interaction partners 1. trimeric mutant TM domain of VEGFR2 receptor, : 30 interactors Detail

More details for 30 interactors identified by 19 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 13C,15N - filtered NOESY-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	VEGFR-2tm769	natural abundance		0.6 mM
2	VEGFR-2tm769	[U-100% 13C; U-100% 15N]		0.6 mM
3	DPC	[U-100% 2H]		120 mM
4	sodium acetate	[U-99% 2H]		20 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19531_2met.nef
Input source #2: Coordindates	2met.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-------
EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRANGG

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

-------110-------120-------130-------
EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRANGG
--------10--------20--------30-------

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

-------210-------220-------230-------
EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRANGG
|||||||||||||||||||||||||||||||||||||
EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRANGG
--------10--------20--------30-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	37	0	0	100.0
B	B	37	0	0	100.0
C	C	37	0	0	100.0

Content subtype: combined_19531_2met.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	451		100.0 (chain: A, length: 37)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	702 (1)	noe	91.9 (chain: A, length: 37), 91.9 (chain: B, length: 37), 91.9 (chain: C, length: 37)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	2172 (2172)	.	97.3 (chain: A, length: 37), 97.3 (chain: B, length: 37), 97.3 (chain: C, length: 37)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 236
  - ¹³C chemical shifts: 171
  - ¹⁵N chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 91.9%
  - Entity_assembly_ID: B, Chain length: 37, Sequence coverage: 91.9%
  - Entity_assembly_ID: C, Chain length: 37, Sequence coverage: 91.9%
- Total number of restraints: 702
- Weight of restraints: 1.0 (702)
- Potential type of restraints: upper-bound-parabolic (702)
- Range of distance target values: 0.0, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 97.3%
  - Entity_assembly_ID: B, Chain length: 37, Sequence coverage: 97.3%
  - Entity_assembly_ID: C, Chain length: 37, Sequence coverage: 97.3%
- Total number of restraints: 2172
- Total number of restraints per polymer type: 2172
- Weight of restraints: 1.0 (2172)
- Potential type of restraints: square-well-parabolic (2172)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

Keywords dimer, homodimer, receptor tyrosine kinase, VEGFR2