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BMRB: 18980

2M3Z

NMR solution structure of HIV-1 nucleocapsid protein in complex with an inhibitor displaying a 2 inhibitors:1 NC stoichiometry

Authors

Goudreau, N., Hucke, O.

Assembly

NC inhibitor 3 complex

Entity

1. NC inhibitor 3 complex, entity 1 (polymer, Thiol state: all other bound), 55 monomers, 6351.318 Da Detail

IQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

2. NC inhibitor 3 complex, entity ZN (non-polymer), 65.409 × 2 Da
3. (3E)-3-{(2Z)-[(5Z)-5-(furan-2-ylmethylidene)-4-oxo-1,3-thiazolidin-2-ylidene]hydrazinylidene}-2-oxo-2,3-dihydro-1H-indole-5-sulfonic acid (non-polymer), 418.404 × 2 Da

Total weight

7318.944 Da

Max. entity weight

6351.318 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS15:SG	2:ZN1:ZN
2	na	sing	1:CYS18:SG	2:ZN1:ZN
3	na	sing	1:CYS28:SG	2:ZN1:ZN
4	na	sing	1:HIS23:NE2	2:ZN1:ZN
5	na	sing	1:CYS36:SG	2:ZN1:ZN
6	na	sing	1:CYS39:SG	2:ZN1:ZN
7	na	sing	1:CYS49:SG	2:ZN1:ZN
8	na	sing	1:HIS44:NE2	2:ZN1:ZN

Source organism

Human immunodeficiency virus 1

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.1 %, Completeness (bb): 83.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.1 % (572 of 664)	97.8 % (353 of 361)	65.7 % (157 of 239)	96.9 % (62 of 64)
Backbone	83.5 % (274 of 328)	99.1 % (114 of 115)	67.3 % (107 of 159)	98.1 % (53 of 54)
Sidechain	90.1 % (347 of 385)	97.2 % (239 of 246)	76.7 % (99 of 129)	90.0 % (9 of 10)
Aromatic	52.5 % (21 of 40)	100.0 % (20 of 20)	0.0 % (0 of 19)	100.0 % (1 of 1)
Methyl	95.5 % (21 of 22)	100.0 % (11 of 11)	90.9 % (10 of 11)

1. entity 1

IQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 25 mM sodium phosphate (pH 6.5) in 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NC inhibitor 3	[U-100% 13C; U-100% 15N]	250 (±50.0) uM
2	3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE	natural abundance	500 (±10.0) uM
3	sodium phosphate	natural abundance	25 (±10.0) mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.56 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 2.56 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M3Z, Strand ID: A Detail

Release date

2013-02-20

Citation

Discovery and structural characterization of a new inhibitor series of HIV-1 nucleocapsid function: NMR solution structure determination of a ternary complex involving a 2:1 inhibitor/NC stoichiometry
Goudreau, N., Hucke, O., Faucher, A., Grand-Maitre, C., Lepage, O., Bonneau, P.R., Mason, S.W., Titolo, S.
J. Mol. Biol. (2013), 425, 1982-1998, PubMed 23485336 , DOI 10.1016/j.jmb.2013.02.022 , Abstract

Related entities 1. NC inhibitor 3 complex, entity 1, : 1 : 3 : 11 : 161 entities Detail

Interaction partners 1. NC inhibitor 3 complex, entity 1, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 3D HNCA