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BMRB: 16466

2KNF

Solution structure and functional characterization of human plasminogen kringle 5

Authors

Battistel, M.D., Grishaev, A., An, S.A., Castellino, F.J., Llinas, M.

Assembly

plasminogen kringle 5

Entity

1. plasminogen kringle 5 (polymer, Thiol state: all disulfide bound), 86 monomers, 9557.483 Da Detail

SNADCMFGNG KGYRGKRVTT VTGTPCQDWA AQEPHRHSIF TPETNPRAGL EKNYCRNPDG DVGGPWCYTT NPRKLYDYCD VPQCAA

Formula weight

9557.483 Da

Source organism

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.1 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	87.1 % (512 of 588)	85.0 % (424 of 499)	98.9 % (88 of 89)
Backbone	98.0 % (246 of 251)	97.7 % (169 of 173)	98.7 % (77 of 78)
Sidechain	78.3 % (264 of 337)	77.6 % (253 of 326)	100.0 % (11 of 11)
Aromatic	91.7 % (44 of 48)	91.3 % (42 of 46)	100.0 % (2 of 2)
Methyl	96.4 % (27 of 28)	96.4 % (27 of 28)

1. rK5

SNADCMFGNG KGYRGKRVTT VTGTPCQDWA AQEPHRHSIF TPETNPRAGL EKNYCRNPDG DVGGPWCYTT NPRKLYDYCD VPQCAA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2KNF, Strand ID: A Detail

Release date

2009-12-10

Citation

Solution structure and functional characterization of human plasminogen kringle 5
Battistel, M.D., Grishaev, A., An, S., Castellino, F.J., Llinas, M.
Biochemistry (2009), 48, 10208-10219, PubMed 19821587 , DOI 10.1021/bi901433n , Abstract

Related entities 1. plasminogen kringle 5, : 1 : 6 : 453 entities Detail

Interaction partners 1. plasminogen kringle 5, : 36 interactors Detail

More details for 36 interactors identified by 15 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

2 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

3 2D DQF-COSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

4 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

5 3D HNHA

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

6 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

7 3D 1H-15N TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	sodium phosphate	natural abundance		50 mM
4	AMCHA	natural abundance		11 mM
5	rK5	natural abundance		2.2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16466_2knf.nef
Input source #2: Coordindates	2knf.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	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:1:CYS:SG	A:80:CYS:SG	unknown	unknown	2.032
A:22:CYS:SG	A:63:CYS:SG	unknown	unknown	2.026
A:51:CYS:SG	A:75:CYS:SG	unknown	unknown	2.021

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	.	Not matched with CCD	None

Sequence alignments

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

------                                                                                 
.SNADC                                                                                 
 |||||                                                                                 
-SNADCMFGNGKGYRGKRVTTVTGTPCQDWAAQEPHRHSIFTPETNPRAGLEKNYCRNPDGDVGGPWCYTTNPRKLYDYCDVPQCAA
 ---------10--------20--------30--------40--------50--------60--------70--------80-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	86	1	0	100.0

Content subtype: combined_16466_2knf.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	516		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3051	noe	No information
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Error	56	hbond	No information
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	57	.	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Error
  - Experiment type: hbond

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .

Keywords Protein