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BMRB: 25394

2MX6

complex structure of Dvl PDZ domain with ligand

Authors

Zhang, X., Zheng, J.J.

Assembly

complex of Dvl PDZ domain with ligand

Entity

1. complex of Dvl PDZ domain with ligand, entity 1 (polymer, Thiol state: not present), 90 monomers, 9623.812 Da Detail

NIITVTLNME RHHFLGISIV GQSNDRGDGG IYIGSIMKGG AVAADGRIEP GDMLLQVNDV NFENMSNDDA VRVLREIVSQ TGPISLTVAK

2. complex of Dvl PDZ domain with ligand, entity 2 (polymer, Thiol state: not present), 3 monomers, 455.9334 Da Detail

XWV

Total weight

10079.745 Da

Max. entity weight

9623.812 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 18.3 %, Completeness: 7.5 %, Completeness (bb): 4.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	7.5 % (69 of 918)	8.0 % (42 of 523)	6.8 % (27 of 395)
Backbone	4.4 % (20 of 458)	3.1 % (6 of 193)	5.3 % (14 of 265)
Sidechain	11.1 % (60 of 541)	10.9 % (36 of 330)	11.4 % (24 of 211)
Aromatic	10.6 % (5 of 47)	20.8 % (5 of 24)	0.0 % (0 of 23)
Methyl	16.4 % (20 of 122)	18.0 % (11 of 61)	14.8 % (9 of 61)

1. entity 1

NIITVTLNME RHHFLGISIV GQSNDRGDGG IYIGSIMKGG AVAADGRIEP GDMLLQVNDV NFENMSNDDA VRVLREIVSQ TGPISLTVAK

2. entity 2

XWV

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_2	natural abundance	10 mM
3	potassium phosphate	natural abundance	100 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MX6, Strand ID: A Detail

Release date

2015-12-27

Citation

Protein-ligand interaction decoded by NMR chemical shift analysis
Zhang, X., Zheng, J.J.
Not known

Related entities 1. complex of Dvl PDZ domain with ligand, entity 1, : 4 : 3 : 2 : 186 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25394_2mx6.nef
Input source #2: Coordindates	2mx6.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)
2:1:PHQ:C1	2:2:TRP:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	PHQ	benzyl chlorocarbonate	Assigned chemical shifts, Coordinates

Sequence alignments

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

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

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

---
XWV
|||
XWV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0
B	B	3	0	0	100.0

Content subtype: combined_25394_2mx6.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	63		15.6 (chain: A, length: 90), 100.0 (chain: B, length: 3)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	37 (1)	noe	8.9 (chain: A, length: 90), 66.7 (chain: B, length: 3)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1 (1)	hbond	33.3 (chain: B, length: 3)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 15.6%
  - Entity_assembly_ID: B, Chain length: 3, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 39
  - ¹³C chemical shifts: 24
- Completeness of assignments
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID
1	PHQ

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	12	80.0
¹³C chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	3	75.0
¹³C chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	9	81.8
¹³C chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0
¹³C chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	5	83.3
¹³C chemical shifts	5	0	0.0

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: 90, Sequence coverage: 8.9%
  - Entity_assembly_ID: B, Chain length: 3, Sequence coverage: 66.7%
- Total number of restraints: 37
- Weight of restraints: 1.0 (37)
- Potential type of restraints: square-well-parabolic (37)
- Range of distance target values: 2.3, 4.15 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 3, Sequence coverage: 33.3%
  - Total number of restraints: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Range of distance target values: 2.0, 2.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords Dvl, PDZ

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Found 1 Document (0.656 seconds)

BMRB: 25394

Sample

Related entities 1. complex of Dvl PDZ domain with ligand, entity 1, : 4 : 3 : 2 : 186 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail