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BMRB: 25536

2N0U

MDMX-057

Authors

Grace, C.R., Kriwacki, R.W.

Assembly

MDMX-057

Entity

1. MDMX-057, entity 1 (polymer, Thiol state: all free), 89 monomers, 10148.80 Da Detail

QINQVRPKLP LLKILHAAGA QGEMFTVKEV MHYLGQYIMV KQLYDQQEQH MVYCGGDLLG ELLGRQSFSV KDPSPLYDML RKNLVTLAT

2. MDMX-057, entity CM7 (non-polymer), 628.705 Da

Total weight

10777.505 Da

Max. entity weight

10148.8 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.8 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.8 % (1045 of 1080)	95.0 % (537 of 565)	98.6 % (413 of 419)	99.0 % (95 of 96)
Backbone	97.7 % (514 of 526)	95.6 % (173 of 181)	98.5 % (256 of 260)	100.0 % (85 of 85)
Sidechain	96.4 % (613 of 636)	94.8 % (364 of 384)	99.2 % (239 of 241)	90.9 % (10 of 11)
Aromatic	100.0 % (72 of 72)	100.0 % (36 of 36)	100.0 % (36 of 36)
Methyl	98.2 % (108 of 110)	100.0 % (55 of 55)	96.4 % (53 of 55)

1. entity 1

QINQVRPKLP LLKILHAAGA QGEMFTVKEV MHYLGQYIMV KQLYDQQEQH MVYCGGDLLG ELLGRQSFSV KDPSPLYDML RKNLVTLAT

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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2N0U, Strand ID: A Detail

Release date

2016-01-24

Citation

Monitoring ligand-induced protein ordering in drug discovery
Grace, C., Kriwacki, R.
J. Mol. Biol. (2016), PubMed 26812210 , DOI 10.1016/j.jmb.2016.01.016 , Abstract

Related entities 1. MDMX-057, entity 1, : 1 : 24 : 9 : 83 entities Detail

Interaction partners 1. MDMX-057, entity 1, : 29 interactors Detail

More details for 29 interactors identified by 12 citations

Experiments performed 13 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 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

4 3D HNCA

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

5 3D HNCACB

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

7 3D C(CO)NH

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

8 3D HNCO

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

13 3D HN(CA)CO

Instrument

Bruker Avance - 600 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	entity_1	[U-100% 13C; U-100% 15N]		0.5 mM
2	entity_2	natural abundance		0.6 mM
3	NaCl	natural abundance		200 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25536_2n0u.nef
Input source #2: Coordindates	2n0u.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	48M	4-[(4S,5R)-4-(3-chlorophenyl)-5-(4-chlorophenyl)-1-(3-oxidanylidenepiperazin-1-yl)carbonyl-4,5-dihydroimidazol-2-yl]-3-propan-2-yloxy-benzenecarbonitrile	None
B	200	CM7	N-[(1S,2R)-1-benzyl-2-hydroxy-3-{[3-(trifluoromethyl)benzyl]amino}propyl]-7-ethyl-1-methyl-3,4-dihydro-1H-[1,2,5]thiadiazepino[3,4,5-hi]indole-9-carboxamide 2,2-dioxide	Assigned chemical shifts

Sequence alignments

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

------30--------40--------50--------60--------70--------80--------90-------100-------110-
QINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT
--------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	89	0	0	100.0

Content subtype: combined_25536_2n0u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1092		100.0 (chain: A, length: 89), 50.0 (chain: B, length: 2)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	395 (1)	noe	97.8 (chain: A, length: 89)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	2262 (1)	noe	100.0 (chain: A, length: 89)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	38 (1)	hbond	38.2 (chain: A, length: 89)
4	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	80 (1)	hbond	39.3 (chain: A, length: 89)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	87 (87)	.	71.9 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
- Total number of assignments
  - ¹H chemical shifts: 584
  - ¹³C chemical shifts: 413
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: 89, Sequence coverage: 97.8%
- Total number of restraints: 395
- Weight of restraints: 1.0 (395)
- Potential type of restraints: upper-bound-parabolic (395)
- Range of distance target values: 2.4, 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
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 100.0%
  - Total number of restraints: 2247
  - Weight of restraints: 1.0 (2247)
  - Potential type of restraints: upper-bound-parabolic (2247)
  - Range of distance target values: 2.31, 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
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 38.2%
    - Total number of restraints: 38
    - Weight of restraints: 1.0 (38)
    - Potential type of restraints: upper-bound-parabolic (38)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_6
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 39.3%
      - Total number of restraints: 80
        Total hydrogen bond restraints: 80
        O...H-x (too close!): 20
        O...h-N (too close!): 20
        O...H-x: 20
        O...h-N: 20
      - Weight of restraints: 1.0 (80)
        Total hydrogen bond restraints: 1.0 (80)
        O...H-x (too close!): 1.0 (20)
        O...h-N (too close!): 1.0 (20)
        O...H-x: 1.0 (20)
        O...h-N: 1.0 (20)
      - Potential type of restraints: upper-bound-parabolic (80)
        Total hydrogen bond restraints: upper-bound-parabolic (80)
        O...H-x (too close!): upper-bound-parabolic (20)
        O...h-N (too close!): upper-bound-parabolic (20)
        O...H-x: upper-bound-parabolic (20)
        O...h-N: upper-bound-parabolic (20)
      - Range of distance target values: 1.8, 3.0 (Å)
      - Histogram of distance target values
      - Histogram of discrepancy in distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 71.9%
- Total number of restraints: 87
- Total number of restraints per polymer type: 87
- Weight of restraints: 1.0 (87)
- Potential type of restraints: square-well-parabolic (87)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MDMX, p53