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Found 1 Document (1.4 seconds)

BMRB: 25808

2N7K

Unveiling the structural determinants of KIAA0323 binding preference for NEDD8

Authors

Santonico, E., Nepravishta, R., Mattioni, A., Valentini, E., Mandaliti, W., Procopio, R., Iannuccelli, M., Castagnoli, L., Polo, S., Paci, M., Cesareni, G.

Assembly

KIAA0323 binding with NEDD8

Entity

1. KIAA0323 binding with NEDD8, entity 1 (polymer, Thiol state: not present), 76 monomers, 8559.861 Da Detail

MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG

2. KIAA0323 binding with NEDD8, entity 2 (polymer), 52 monomers, 6289.104 Da Detail

GGIRKTRETE RLRRQLLEVF WGQDHKVDFI LQREPYCRDI NQLSEALLSL NF

Total weight

14848.965 Da

Max. entity weight

8559.861 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 25.4 %, Completeness (bb): 62.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	25.4 % (245 of 964)	15.1 % (125 of 828)	88.2 % (120 of 136)
Backbone	62.2 % (240 of 386)	45.8 % (120 of 262)	96.8 % (120 of 124)
Sidechain	0.9 % (5 of 578)	0.9 % (5 of 566)	0.0 % (0 of 12)
Aromatic	0.0 % (0 of 38)	0.0 % (0 of 37)	0.0 % (0 of 1)
Methyl	0.0 % (0 of 78)	0.0 % (0 of 78)

1. entity 1

MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG

2. entity 2

GGIRKTRETE RLRRQLLEVF WGQDHKVDFI LQREPYCRDI NQLSEALLSL NF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 15N]		0.15 ~ 1.5 mM
2	entity_2	[U-100% 15N]		0.15 ~ 1.5 mM

Protein Blocks Logo

Calculated from 11 models in PDB: 2N7K, Strand ID: A, B Detail

Release date

2016-09-07

Citation

Unveiling the structural determinants of KIAA0323 binding preference for NEDD8
Santonico, E., Nepravishta, R., Mattioni, A., Valentini, E., Mandaliti, W., Procopio, R., Iannuccelli, M., Castagnoli, L., Polo, S., Paci, M., Cesareni, G.
Not known

Related entities 1. KIAA0323 binding with NEDD8, entity 1, : 8 : 1 : 276 entities Detail

Related entities 2. KIAA0323 binding with NEDD8, entity 2, : 1 : 4 : 6 entities Detail

Interaction partners 2. KIAA0323 binding with NEDD8, entity 2, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 5 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25808_2n7k.nef
Input source #2: Coordindates	2n7k.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-
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGGLRQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGGLRQ

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

--80--------90-------100-------110-------120--------
GGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF
||||||||||||||||||||||||||||||||||||||||||||||||||||
GGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF
--------10--------20--------30--------40--------50--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0
B	B	52	0	0	100.0

Content subtype: combined_25808_2n7k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	238		86.4 (chain: A, length: 81), 96.2 (chain: B, length: 52)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1896 (1)	noe	90.1 (chain: A, length: 81), 51.9 (chain: B, length: 52)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	229 (1)	noe	11.1 (chain: A, length: 81), 82.7 (chain: B, length: 52)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	82 (1)	hbond	65.4 (chain: A, length: 81)
4	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	40 (1)	hbond	57.7 (chain: B, length: 52)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	158 (158)	.	79.0 (chain: A, length: 81), 82.7 (chain: B, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 86.4%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 96.2%
- Total number of assignments
  - ¹⁵N chemical shifts: 120
  - ¹H chemical shifts: 118
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	89	70	78.7
¹H chemical shifts	512	69	13.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	78	70	89.7
¹H chemical shifts	168	69	41.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	11	0	0.0
¹H chemical shifts	344	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	65	50	76.9
¹H chemical shifts	346	49	14.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	51	50	98.0
¹H chemical shifts	106	49	46.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	14	0	0.0
¹H chemical shifts	240	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	1	0	0.0
¹H chemical shifts	27	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 90.1%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 51.9%
- Total number of restraints: 1887
- Weight of restraints: 1.0 (1887)
- Potential type of restraints: square-well-parabolic (1887)
- Range of distance target values: 1.35, 4.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 11.1%
    - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 82.7%
  - Total number of restraints: 229
  - Weight of restraints: 1.0 (229)
  - Potential type of restraints: square-well-parabolic (229)
  - Range of distance target values: 1.8, 9.6 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_2
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 65.4%
    - Total number of restraints: 82
    - Weight of restraints: 1.0 (82)
    - Potential type of restraints: square-well-parabolic (82)
    - Range of distance target values: 1.9, 3.05 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_4
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 57.7%
        --80--------90-------100-------110-------120-------- GGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF ||||||||| | | | | ||||||||||||||||| .....TRETERLRR....V...Q..K...I.....YCRDINQLSEALLSLNF
      - Total number of restraints: 40
        Total hydrogen bond restraints: 40
        O...h-N: 20
        O...H-x: 20
      - Weight of restraints: 1.0 (40)
        Total hydrogen bond restraints: 1.0 (40)
        O...h-N: 1.0 (20)
        O...H-x: 1.0 (20)
      - Potential type of restraints: square-well-parabolic (40)
        Total hydrogen bond restraints: square-well-parabolic (40)
        O...h-N: square-well-parabolic (20)
        O...H-x: square-well-parabolic (20)
      - Range of distance target values: 2.0, 2.95 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        None
        Chain_ID: B
      - Distance restraints on contact map
        Chain_ID_1: B - Chain_ID_2: B

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 79.0%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 82.7%
- Total number of restraints: 158
- Total number of restraints per polymer type: 158
- Weight of restraints: 1.0 (158)
- Potential type of restraints: square-well-parabolic (158)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords KIAA0323, NEDD8, Protein

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Found 1 Document (1.4 seconds)

BMRB: 25808

Sample

Related entities 1. KIAA0323 binding with NEDD8, entity 1, : 8 : 1 : 276 entities Detail

Related entities 2. KIAA0323 binding with NEDD8, entity 2, : 1 : 4 : 6 entities Detail

Interaction partners 2. KIAA0323 binding with NEDD8, entity 2, : 2 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail