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BMRB: 25008

2MQ1

Phosphotyrosine binding domain

Authors

Mukherjee, M.DR., Jing-Song, F.DR., Sivaraman, J.DR.

Assembly

Phosphotyrosine binding domain

Entity

1. Phosphotyrosine binding domain, entity 1 (polymer), 89 monomers, 10198.98 Da Detail

VHFCDKCGLP IKVYGRMIPC KHVFCYDCAI LHEKKGDKMC PGCSDPVQRI EQCTRGSLFM CSIVQGCKRT YLSQRDLQAH INHRHMRAG

2. ZINC ION (non-polymer), 65.409 × 3 Da

Total weight

10395.207 Da

Max. entity weight

10198.98 Da

Entity Connection

metal coordination 12 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS4:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS7:SG	2:ZN1:ZN
3	metal coordination	sing	1:CYS25:SG	2:ZN1:ZN
4	metal coordination	sing	1:CYS28:SG	2:ZN1:ZN
5	metal coordination	sing	1:CYS20:SG	2:ZN1:ZN
6	metal coordination	sing	1:HIS22:SG	2:ZN1:ZN
7	metal coordination	sing	1:CYS40:SG	2:ZN1:ZN
8	metal coordination	sing	1:CYS43:SG	2:ZN1:ZN
9	metal coordination	sing	1:CYS61:SG	2:ZN1:ZN
10	metal coordination	sing	1:CYS67:SG	2:ZN1:ZN
11	metal coordination	sing	1:HIS80:SG	2:ZN1:ZN
12	metal coordination	sing	1:HIS85:SG	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 62.5 %, Completeness (bb): 58.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	62.5 % (652 of 1043)	84.5 % (465 of 550)	24.6 % (99 of 402)	96.7 % (88 of 91)
Backbone	58.4 % (307 of 526)	98.9 % (179 of 181)	17.7 % (46 of 260)	96.5 % (82 of 85)
Sidechain	60.8 % (364 of 599)	77.5 % (286 of 369)	32.1 % (72 of 224)	100.0 % (6 of 6)
Aromatic	33.3 % (26 of 78)	46.2 % (18 of 39)	20.5 % (8 of 39)
Methyl	100.0 % (74 of 74)	100.0 % (37 of 37)	100.0 % (37 of 37)

1. entity 1

VHFCDKCGLP IKVYGRMIPC KHVFCYDCAI LHEKKGDKMC PGCSDPVQRI EQCTRGSLFM CSIVQGCKRT YLSQRDLQAH INHRHMRAG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MQ1, Strand ID: A Detail

Release date

2014-08-03

Citation

Dimeric switch of Hakai-truncated monomers during substrate recognition: insights from solution studies and NMR structure
Mukherjee, M.DR., Jing-Song, F.DR., Sivaraman, J.DR.
J. Biol. Chem. (2014), 289, 25611-25623, PubMed 25074933 , DOI 10.1074/jbc.M114.592840 , Abstract

Related entities 1. Phosphotyrosine binding domain, entity 1, : 1 : 4 : 3 : 19 entities Detail

Interaction partners 1. Phosphotyrosine binding domain, entity 1, : 12 interactors Detail

More details for 12 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

6 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

7 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

10 3D HN(COCA)CB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]		1 mM
2	DTT	natural abundance		5 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %
5	potassium phosphate	natural abundance		50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25008_2mq1.nef
Input source #2: Coordindates	2mq1.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:80:HIS:NE2	2:3:ZN:ZN	unknown	unknown	n/a
1:85:HIS:NE2	2:3:ZN:ZN	unknown	unknown	n/a
1:22:HIS:ND1	2:2:ZN:ZN	unknown	unknown	n/a
1:25:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:43:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:7:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:61:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:67:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:20:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:28:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:40:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:4:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None
B	3	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80---------
VHFCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRAG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VHFCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRAG

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_25008_2mq1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	610		100.0 (chain: A, length: 89)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1484 (1)	noe	98.9 (chain: A, length: 89)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	38 (1)	hbond	30.3 (chain: A, length: 89)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	67 (67)	.	50.6 (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%
- Total number of assignments
  - ¹H chemical shifts: 458
  - ¹³C chemical shifts: 63
  - ¹⁵N chemical shifts: 89
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 98.9%
- Total number of restraints: 1484
- Weight of restraints: 1.0 (1484)
- Potential type of restraints: square-well-parabolic (1484)
- Range of distance target values: 2.35, 5.6 (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: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 30.3%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 2.0, 2.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 50.6%
- Total number of restraints: 67
- Total number of restraints per polymer type: 67
- Weight of restraints: 1.0 (67)
- Potential type of restraints: square-well-parabolic (67)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords phosphotyrosine binding