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BMRB: 19230

2M86

Solution structure of Hdm2 with engineered cyclotide

Authors

Majumder, S., Ji, Y., Millard, M., Borra, R., Bi, T., Elnagar, A.Y., Neamati, N., Camarero, J.A.

Assembly

Hdm2

Entity

1. Hdm2 (polymer, Thiol state: all disulfide bound), 51 monomers, 5284.948 Da Detail

SGSGASKAPT SFAEYWNLLS AGGVCPKILQ RCRRDSDCPG ACICRGNGYC G

2. MCo-PMI (polymer), 83 monomers, 9799.543 Da Detail

LVRPKPLLLK LLKSVGAQKD TYTMKEVLFY LGQYIMTKRL YDEKQQHIVY CSNDLLGDLF GVPSFSVKEH RKIYTMIYRN LVV

Total weight

15084.491 Da

Max. entity weight

9799.543 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS38:SG	1:CYS50:SG
2	disulfide	sing	1:CYS32:SG	1:CYS44:SG
3	disulfide	sing	1:CYS25:SG	1:CYS42:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 52.7 %, Completeness (bb): 67.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.7 % (836 of 1586)	65.5 % (542 of 828)	27.7 % (172 of 620)	88.4 % (122 of 138)
Backbone	67.7 % (536 of 792)	91.2 % (250 of 274)	42.3 % (165 of 390)	94.5 % (121 of 128)
Sidechain	40.9 % (375 of 916)	52.7 % (292 of 554)	23.3 % (82 of 352)	10.0 % (1 of 10)
Aromatic	3.8 % (5 of 132)	6.1 % (4 of 66)	0.0 % (0 of 65)	100.0 % (1 of 1)
Methyl	25.3 % (37 of 146)	42.5 % (31 of 73)	8.2 % (6 of 73)

1. Hdm2

SGSGASKAPT SFAEYWNLLS AGGVCPKILQ RCRRDSDCPG ACICRGNGYC G

2. MCo-PMI

LVRPKPLLLK LLKSVGAQKD TYTMKEVLFY LGQYIMTKRL YDEKQQHIVY CSNDLLGDLF GVPSFSVKEH RKIYTMIYRN LVV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MCo-PMI	natural abundance	0.2 mM
2	Hdm2	[U-99% 13C; U-99% 15N]	0.2 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	MCo-PMI	[U-99% 15N]	0.2 mM
6	Hdm2	natural abundance	0.2 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MCo-PMI	natural abundance	0.2 mM
10	Hdm2	natural abundance	0.2 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	acetate	methyl carbon	21.03 ppm	na	indirect	1.0
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0
¹⁵N	urea	nitrogen	73.4 ppm	na	indirect	1.0

Referencing offset: 1.57 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	acetate	methyl carbon	21.03 ppm	na	indirect	1.0
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0
¹⁵N	urea	nitrogen	73.4 ppm	na	indirect	1.0

Referencing offset: 1.57 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	acetate	methyl carbon	21.03 ppm	na	indirect	1.0
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0
¹⁵N	urea	nitrogen	73.4 ppm	na	indirect	1.0

Referencing offset: 0.17 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M86, Strand ID: A, B Detail

Release date

2013-07-28

Citation

In vivo activation of the p53 tumor suppressor pathway by an engineered cyclotide
Ji, Y., Majumder, S., Millard, M., Borra, R., Bi, T., Elnagar, A.Y., Neamati, N., Shekhtman, A., Camarero, J.A.
J. Am. Chem. Soc. (2013), 135, 11623-11633, PubMed 23848581 , DOI 10.1021/ja405108p , Abstract

Related entities 1. Hdm2, : 1 entities Detail

Related entities 2. MCo-PMI, : 2 : 3 : 18 entities Detail

Interaction partners 2. MCo-PMI, : 170 interactors Detail

More details for 170 interactors identified by 57 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC