BMRBj - BMREntryMaster

Found 1 Document (2.144 seconds)

BMRB: 16063

2KBX

Solution structure of ILK/PINCH complex

Authors

Qin, J.

Assembly

ILK/PINCH complex

Entity

1. ILK (polymer, Thiol state: all free), 171 monomers, 19352.69 Da Detail

MDDIFTQCRE GNAVAVRLWL DNTENDLNQG DDHGFSPLHW ACREGRSAVV EMLIMRGARI NVMNRGDDTP LHLAASHGHR DIVQKLLQYK ADINAVNEHG NVPLHYACFW GQDQVAEDLV ANGALVSICN KYGEMPVDKA KAPLRELLRE RAEKMGQNLN RIPYKDTFWK G

2. PINCH (polymer, Thiol state: free and other bound), 70 monomers, 7955.964 Da Detail

MANALASATC ERCKGGFAPA EKIVNSNGEL YHEQCFVCAQ CFQQFPEGLF YEFEGRKYCE HDFQMLFAPC

3. ZN (non-polymer), 65.409 × 2 Da

Total weight

27439.47 Da

Max. entity weight

19352.69 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.9 %, Completeness (bb): 85.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.9 % (2509 of 2790)	98.1 % (1425 of 1453)	76.4 % (820 of 1073)	100.0 % (264 of 264)
Backbone	85.3 % (1218 of 1428)	100.0 % (491 of 491)	70.2 % (495 of 705)	100.0 % (232 of 232)
Sidechain	95.5 % (1514 of 1585)	97.1 % (934 of 962)	92.7 % (548 of 591)	100.0 % (32 of 32)
Aromatic	87.3 % (227 of 260)	96.2 % (125 of 130)	77.8 % (98 of 126)	100.0 % (4 of 4)
Methyl	99.6 % (225 of 226)	100.0 % (113 of 113)	99.1 % (112 of 113)

1. ILK

MDDIFTQCRE GNAVAVRLWL DNTENDLNQG DDHGFSPLHW ACREGRSAVV EMLIMRGARI NVMNRGDDTP LHLAASHGHR DIVQKLLQYK ADINAVNEHG NVPLHYACFW GQDQVAEDLV ANGALVSICN KYGEMPVDKA KAPLRELLRE RAEKMGQNLN RIPYKDTFWK G

2. PINCH

MANALASATC ERCKGGFAPA EKIVNSNGEL YHEQCFVCAQ CFQQFPEGLF YEFEGRKYCE HDFQMLFAPC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	0.1-0.5 mM
2	entity_1	[U-100% 13C; U-100% 15N]	0.1-0.5 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.71 ppm	internal	direct	1.0
¹H	water	protons	4.71 ppm	internal	direct	1.0
¹⁵N	water	protons	4.71 ppm	internal	direct	1.0

Referencing offset: 0.25 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.71 ppm	internal	direct	1.0
¹H	water	protons	4.71 ppm	internal	direct	1.0
¹⁵N	water	protons	4.71 ppm	internal	direct	1.0

Referencing offset: 0.25 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.71 ppm	internal	direct	1.0
¹H	water	protons	4.71 ppm	internal	direct	1.0
¹⁵N	water	protons	4.71 ppm	internal	direct	1.0

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-04-15

Citation

Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase
Yang, Y., Wang, X., Hawkins, C.A., Chen, K., Vaynberg, J., Mao, X., Tu, Y., Zuo, X., Wang, J., Wang, Y., Wu, C., Tjandra, N., Qin, J.
J. Biol. Chem. (2009), 284, 5836-5844, PubMed 19117955 , DOI 10.1074/jbc.M805319200 , Abstract

Related entities 1. ILK, : 6 : 1 : 1 : 182 entities Detail

Related entities 2. PINCH, : 1 : 5 : 4 : 232 entities Detail

Interaction partners 1. ILK, : 90 : 1 interactors Detail

More details for 91 interactors identified by 24 citations

Interaction partners 2. PINCH, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 1 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16063_2kbx.nef
Input source #2: Coordindates	2kbx.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	True (see coodinates for details)
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)
B:10:CYS:SG	B:35:CYS:SG	reduced, CA 56.76, CB 30.84 ppm	reduced, CA 60.1, CB 32.5 ppm	2.456

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)
2:10:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:13:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:32:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
2:35:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:38:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:41:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:59:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:62:ASP:OD2	3:2:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	ZN	ZINC ION	None
C	2	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--------90-------100
MDDIFTQCREGNAVAVRLWLDNTENDLNQGDDHGFSPLHWACREGRSAVVEMLIMRGARINVMNRGDDTPLHLAASHGHRDIVQKLLQYKADINAVNEHG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDDIFTQCREGNAVAVRLWLDNTENDLNQGDDHGFSPLHWACREGRSAVVEMLIMRGARINVMNRGDDTPLHLAASHGHRDIVQKLLQYKADINAVNEHG

-------110-------120-------130-------140-------150-------160-------170-
NVPLHYACFWGQDQVAEDLVANGALVSICNKYGEMPVDKAKAPLRELLRERAEKMGQNLNRIPYKDTFWKG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NVPLHYACFWGQDQVAEDLVANGALVSICNKYGEMPVDKAKAPLRELLRERAEKMGQNLNRIPYKDTFWKG

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

--------10--------20--------30--------40--------50--------60--------70
MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	171	0	0	100.0
B	B	70	0	0	100.0

Content subtype: combined_16063_2kbx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	9		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2478		100.0 (chain: A, length: 171), 100.0 (chain: B, length: 70)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1203 (1)	noe	92.9 (chain: B, length: 70)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	46 (1)	hbond	37.1 (chain: B, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 171, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 70, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1426
  - ¹³C chemical shifts: 787
  - ¹⁵N chemical shifts: 265
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
36	SER	HG	5.95
39	HIS	HD1	11.93
72	HIS	HD1	12.01
105	HIS	HD1	11.69

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1028	1004	97.7
¹³C chemical shifts	756	563	74.5
¹⁵N chemical shifts	201	190	94.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	349	347	99.4
¹³C chemical shifts	342	171	50.0
¹⁵N chemical shifts	165	165	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	679	657	96.8
¹³C chemical shifts	414	392	94.7
¹⁵N chemical shifts	36	25	69.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	96	100.0
¹³C chemical shifts	96	91	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	72	97.3
¹³C chemical shifts	70	62	88.6
¹⁵N chemical shifts	4	4	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
32	HIS	HE2	11.23

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	425	415	97.6
¹³C chemical shifts	317	224	70.7
¹⁵N chemical shifts	77	75	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	141	99.3
¹³C chemical shifts	140	70	50.0
¹⁵N chemical shifts	67	67	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	283	274	96.8
¹³C chemical shifts	177	154	87.0
¹⁵N chemical shifts	10	8	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	24	96.0
¹³C chemical shifts	25	24	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	52	92.9
¹³C chemical shifts	56	35	62.5

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: B, Chain length: 70, Sequence coverage: 92.9%
- Total number of restraints: 1203
- Weight of restraints: 1.0 (1203)
- Potential type of restraints: square-well-parabolic (1203)
- Range of distance target values: 2.15, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
  - Chain_ID: C
    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: B, Chain length: 70, Sequence coverage: 37.1%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 1.9, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
    - Chain_ID: C
      None
  - Distance restraints on contact map

Keywords cytoskeletal regulators

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Found 1 Document (2.144 seconds)

BMRB: 16063

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ILK, : 6 : 1 : 1 : 182 entities Detail

Related entities 2. PINCH, : 1 : 5 : 4 : 232 entities Detail

Interaction partners 1. ILK, : 90 : 1 interactors Detail

Interaction partners 2. PINCH, : 2 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 4 contents Detail