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BMRB: 34001

5L3M

D11 bound [S39_PQ]-IGF-II

Authors

Assembly

Insulin-like growth factor II

Entity

1. Insulin-like growth factor II (polymer), 69 monomers, 7700.640 Da Detail

AYRPSETLCG GELVDTLQFV CGDRGFYFSR PASRVSRRSP QRGIVEECCF RSCDLALLET YCATPAKSE

Formula weight

7700.64 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.5 %, Completeness (bb): 79.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.5 % (666 of 770)	98.8 % (396 of 401)	67.2 % (203 of 302)	100.0 % (67 of 67)
Backbone	79.8 % (324 of 406)	100.0 % (139 of 139)	59.4 % (120 of 202)	100.0 % (65 of 65)
Sidechain	94.9 % (406 of 428)	98.1 % (257 of 262)	89.6 % (147 of 164)	100.0 % (2 of 2)
Aromatic	78.1 % (50 of 64)	100.0 % (32 of 32)	56.3 % (18 of 32)
Methyl	100.0 % (62 of 62)	100.0 % (31 of 31)	100.0 % (31 of 31)

1. Insulin-like growth factor II

AYRPSETLCG GELVDTLQFV CGDRGFYFSR PASRVSRRSP QRGIVEECCF RSCDLALLET YCATPAKSE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.59 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.59 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.1 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5L3M, Strand ID: A Detail

Release date

2016-07-31

Citation

Probing Receptor Specificity by Sampling the Conformational Space of the Insulin-like Growth Factor II C-domain
Hexnerova, R., Krizkova, K., Fabry, M., Sieglova, I., Kedrova, K., Collinsova, M., Ullrichova, P., Srb, P., Williams, C., Crump, M.P., Tosner, Z., Jiracek, J., Veverka, V., Zakova, L.
J. Biol. Chem. (2016), 291, 21234-21245, PubMed 27510031 , DOI 10.1074/jbc.M116.741041 , Abstract

Related entities 1. Insulin-like growth factor II, : 1 : 1 : 195 entities Detail

Interaction partners 1. Insulin-like growth factor II, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.2, Details 20 mM d4 acetic acid, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	acetic acid	d4		20 mM
2	H2O	natural abundance		90 %
3	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_34001_5l3m.nef
Input source #2: Coordindates	5l3m.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:9:CYS:SG	A:49:CYS:SG	oxidized, CB 48.505 ppm	oxidized, CB 39.309 ppm	2.03
A:21:CYS:SG	A:62:CYS:SG	oxidized, CB 36.43 ppm	oxidized, CA 53.19, CB 34.459 ppm	2.027
A:48:CYS:SG	A:53:CYS:SG	oxidized, CB 45.084 ppm	oxidized, CA 53.199, CB 47.474 ppm	2.034

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---------
AYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSPQRGIVEECCFRSCDLALLETYCATPAKSE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSPQRGIVEECCFRSCDLALLETYCATPAKSE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0

Content subtype: combined_34001_5l3m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	651		100.0 (chain: A, length: 69)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1635 (1)	noe	100.0 (chain: A, length: 69)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	46 (46)	.	46.4 (chain: A, length: 69)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 396
  - ¹³C chemical shifts: 184
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
- Total number of restraints: 1635
- Weight of restraints: 1.0 (1635)
- Potential type of restraints: square-well-parabolic (1635)
- Range of distance target values: 1.05, 2.75 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 46.4%
- Total number of restraints: 46
- Total number of restraints per polymer type: 46
- Weight of restraints: 1.0 (46)
- Potential type of restraints: square-well-parabolic (46)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords IGF-II, cell cycle