BMRB: 11151

Solution structure of the first Phorbol esters/diacylglycerol binding domain of human Protein kinase C, delta

Authors

Abe, H., Miyamoto, K., Tochio, N., Saito, K., Sasagawa, A., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

Protein kinase C delta type

Entity

1. Phorbol esters/diacylglycerol binding domain (C1 domain) (polymer, Thiol state: all other bound), 83 monomers, 8946.074 Da Detail

GSSGSSGKQA KIHYIKNHEF IATFFGQPTF CSVCKDFVWG LNKQGYKCRQ CNAAIHKKCI DKIIGRCTGT AANSRDTSGP SSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

9076.893 Da

Max. entity weight

8946.074 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS18:ND1	2:ZN1:ZN
2	na	sing	1:CYS48:SG	2:ZN1:ZN
3	na	sing	1:CYS51:SG	2:ZN1:ZN
4	na	sing	1:CYS67:SG	2:ZN1:ZN
5	na	sing	1:CYS31:SG	2:ZN1:ZN
6	na	sing	1:CYS34:SG	2:ZN1:ZN
7	na	sing	1:HIS56:ND1	2:ZN1:ZN
8	na	sing	1:CYS59:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.0 %, Completeness: 86.1 %, Completeness (bb): 82.4 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	86.1 % (806 of 936)	86.3 % (421 of 488)	88.0 % (315 of 358)	77.8 % (70 of 90)
Backbone	82.4 % (407 of 494)	81.6 % (142 of 174)	83.7 % (200 of 239)	80.2 % (65 of 81)
Sidechain	90.3 % (465 of 515)	88.9 % (279 of 314)	94.3 % (181 of 192)	55.6 % (5 of 9)
Aromatic	97.8 % (88 of 90)	97.8 % (44 of 45)	97.7 % (43 of 44)	100.0 % (1 of 1)
Methyl	100.0 % (62 of 62)	100.0 % (31 of 31)	100.0 % (31 of 31)

1. Phorbol esters/diacylglycerol binding domain (C1 domain)

GSSGSSGKQA KIHYIKNHEF IATFFGQPTF CSVCKDFVWG LNKQGYKCRQ CNAAIHKKCI DKIIGRCTGT AANSRDTSGP SSG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05), Details 1.28mM {Protein;} 20mM {d-Tris-HCl;} 100mM {NaCl;} 1mM {d-DTT;} 0.02% NaN3 {;0.05mM} ZnCl2+1mM {IDA;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Phorbol esters/diacylglycerol binding domain (C1 domain)	[U-13C; U-15N]	protein	1.28 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	ZnCl2	natural abundance	salt	0.05 mM
7	IDA	natural abundance	salt	1 mM
8	H2O		solvent	90 %
9	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.1 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.1 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.48 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

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

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Release date

2011-05-04

Citation

Solution structure of the first Phorbol esters/diacylglycerol binding domain of human Protein kinase C, delta
Abe, H., Miyamoto, K., Tochio, N., Saito, K., Sasagawa, A., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Related entities 1. Phorbol esters/diacylglycerol binding domain (C1 domain), : 1 : 3 : 79 entities Detail

Interaction partners 1. Phorbol esters/diacylglycerol binding domain (C1 domain), : 43 interactors Detail

Experiments performed 2 experiments Detail