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BMRB: 17358

2L7J

Solution structure of the third Immunoglobulin-like domain of nectin-1

Authors

Clausen, O., Poulsen, F.M.

Assembly

nectin-1

Entity

1. nectin-1 (polymer), 95 monomers, 10590.66 Da Detail

LNVQYEPEVT IEGFDGNWYL QRTDVKLTCK ADANPPATEY HWTTLNGSLP KGVEAQNRTL FFRGPITYSL AGTYICEATN PIGTRSGQVE VNITH

Formula weight

10590.66 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.7 %, Completeness: 53.8 %, Completeness (bb): 77.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.8 % (585 of 1087)	55.6 % (311 of 559)	44.6 % (190 of 426)	82.4 % (84 of 102)
Backbone	77.4 % (432 of 558)	87.0 % (167 of 192)	65.3 % (181 of 277)	94.4 % (84 of 89)
Sidechain	38.0 % (234 of 616)	39.2 % (144 of 367)	38.1 % (90 of 236)	0.0 % (0 of 13)
Aromatic	0.0 % (0 of 102)	0.0 % (0 of 51)	0.0 % (0 of 49)	0.0 % (0 of 2)
Methyl	41.7 % (45 of 108)	63.0 % (34 of 54)	20.4 % (11 of 54)

1. entity

LNVQYEPEVT IEGFDGNWYL QRTDVKLTCK ADANPPATEY HWTTLNGSLP KGVEAQNRTL FFRGPITYSL AGTYICEATN PIGTRSGQVE VNITH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

LACS Plot; CA

Referencing offset: 0.2 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.2 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L7J, Strand ID: A Detail

Release date

2012-02-14

Citation

Solution structure of the third Immunoglobulin-like domain of nectin-1
Clausen, O., Poulsen, F.M.
Not known

Related entities 1. nectin-1, : 1 : 3 : 242 entities Detail

Interaction partners 1. nectin-1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

2 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

3 3D HNCA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

4 3D HN(CO)CA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

5 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

7 3D H(CCO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

9 3D 1H-15N TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nectin-1	[U-13C; U-15N]		1.0 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 % v/v

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17358_2l7j.nef
Input source #2: Coordindates	2l7j.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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:269:CYS:SG	A:316:CYS:SG	oxidized, CA 55.31, CB 42.28 ppm	oxidized, CA 52.02, CB 44.46 ppm	2.031

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

-------250-------260-------270-------280-------290-------300-------310-------320-------330-----
LNVQYEPEVTIEGFDGNWYLQRTDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFRGPITYSLAGTYICEATNPIGTRSGQVEVNITH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LNVQYEPEVTIEGFDGNWYLQRTDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFRGPITYSLAGTYICEATNPIGTRSGQVEVNITH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_17358_2l7j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	561		93.7 (chain: A, length: 95)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1909 (1)	noe	90.5 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 93.7%
- Total number of assignments
  - ¹H chemical shifts: 307
  - ¹³C chemical shifts: 170
  - ¹⁵N chemical shifts: 84
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 90.5%
- Total number of restraints: 1897
- Weight of restraints: 1.0 (1897)
- Potential type of restraints: upper-bound-parabolic (1897)
- Range of distance target values: 2.2, 5.5 (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

Keywords cellular adhesion molecule, immunoglobulin, nectin, nmr