NMR structure of an inhibitor bound dengue NS3 protease
GSAADLELER AADVKWEDQA EISGSSPILS ITISEDGSMS IKNEEEEQTL GGGGSGGGGE FAGVLWDVPS PPPVGKAELE DGAYRIKQKG ILGYSQIGAG VYKEGTFHTM WHVTRGAVLM HKGKRIEPSW ADVKKDLISY GGGWKLEGEW KEGEEVQVLA LEPGKNPRAV QTKPGLFKTN AGTIGAVSLD FSPGTSGSPI IDKKGKVVGL YGNGVVTRSG AYVSAIAQTE KSIEDNPEIE XKRX
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 50.6 % (1374 of 2717) | 30.3 % (428 of 1414) | 68.7 % (723 of 1053) | 89.2 % (223 of 250) |
Backbone | 76.7 % (1104 of 1440) | 49.9 % (256 of 513) | 91.2 % (634 of 695) | 92.2 % (214 of 232) |
Sidechain | 31.1 % (461 of 1484) | 19.1 % (172 of 901) | 49.6 % (280 of 565) | 50.0 % (9 of 18) |
Aromatic | 7.0 % (12 of 172) | 7.0 % (6 of 86) | 0.0 % (0 of 80) | 100.0 % (6 of 6) |
Methyl | 75.2 % (188 of 250) | 72.0 % (90 of 125) | 78.4 % (98 of 125) |
1. entity 1
GSAADLELER AADVKWEDQA EISGSSPILS ITISEDGSMS IKNEEEEQTL GGGGSGGGGE FAGVLWDVPS PPPVGKAELE DGAYRIKQKG ILGYSQIGAG VYKEGTFHTM WHVTRGAVLM HKGKRIEPSW ADVKKDLISY GGGWKLEGEW KEGEEVQVLA LEPGKNPRAV QTKPGLFKTN AGTIGAVSLD FSPGTSGSPI IDKKGKVVGL YGNGVVTRSG AYVSAIAQTE KSIEDNPEIE XKRX2. ketobenzene
XXKRXSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | entity_1 | [U-5% 13C; U-100% 15N] | 0.8 mM | |
5 | H2O | natural abundance | 95 % | |
6 | D2O | natural abundance | 5 % |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | entity_1 | [U-13C; U-15N; U-2H];[1H-13C]-I(delta1)LVM | 0.8 mM | |
8 | H2O | natural abundance | 95 % | |
9 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N; U-2H] | 0.8 mM | |
2 | H2O | natural abundance | 95 % | |
3 | D2O | natural abundance | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_19306_2m9q.nef |
Input source #2: Coordindates | 2m9q.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
NoneOther 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:BEZ:C | 2:2:NLE:N | unknown | unknown | n/a |
2:2:NLE:C | 2:3:LYS:N | unknown | unknown | n/a |
2:4:ARG:C | 2:5:M9P:N | unknown | unknown | n/a |
1:196:SER:OG | 2:5:M9P:CI | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 251 | BEZ | BENZOIC ACID | Assigned chemical shifts, Coordinates |
B | 252 | NLE | NORLEUCINE | Assigned chemical shifts, Coordinates |
B | 255 | M9P | amino{[(4S,5S)-4-amino-6,6,6-trifluoro-5-hydroxyhexyl]amino}methaniminium | Assigned chemical shifts, Coordinates |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI -------210-------220-------230-------240 IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE |||||||||||||||||||||||||||||||||||||||| IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE
----- XXKRX ||||| XXKRX
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 240 | 0 | 0 | 100.0 |
B | B | 5 | 0 | 0 | 100.0 |
Content subtype: combined_19306_2m9q.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG ||||||||||||||||||||||||||||||||||||||||| |||||| ||| |||||||||||| ||||| | |||||||||||||||||||| .SAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIK...EEQTLG..GSG..GEFAGVLWDVPS..PVGKA.L.DGAYRIKQKGILGYSQIGAG -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI ||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| VYKEGTFHTMWHVTRGAVLMHKGKRIE.SWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFS.GTSGSPI -------210-------220-------230-------240 IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE ||||||||||||||||| |||||||||||||||||||||| IDKKGKVVGLYGNGVVT.SGAYVSAIAQTEKSIEDNPEIE
----- XXKRX ||||| XXKRX
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
23 | SER | HG | 6.173 |
25 | SER | HG | 6.169 |
34 | SER | HG | 6.167 |
40 | SER | HG | 6.06 |
109 | THR | HG1 | 6.637 |
114 | THR | HG1 | 4.888 |
129 | SER | HG | 4.287 |
172 | THR | HG1 | 6.174 |
179 | THR | HG1 | 6.114 |
192 | SER | HG | 6.327 |
195 | THR | HG1 | 6.324 |
198 | SER | HG | 5.972 |
217 | THR | HG1 | 5.127 |
224 | SER | HG | 5.289 |
229 | THR | HG1 | 6.343 |
232 | SER | HG | 6.117 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 1031 | 712 | 69.1 |
1H chemical shifts | 1376 | 310 | 22.5 |
15N chemical shifts | 252 | 217 | 86.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 480 | 438 | 91.2 |
1H chemical shifts | 505 | 210 | 41.6 |
15N chemical shifts | 228 | 208 | 91.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 551 | 274 | 49.7 |
1H chemical shifts | 871 | 100 | 11.5 |
15N chemical shifts | 24 | 9 | 37.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 128 | 101 | 78.9 |
1H chemical shifts | 128 | 84 | 65.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 80 | 0 | 0.0 |
1H chemical shifts | 86 | 6 | 7.0 |
15N chemical shifts | 6 | 6 | 100.0 |
Comp_index_ID | Comp_ID |
---|---|
251 | BEZ |
255 | M9P |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 12 | 0 | 0.0 |
1H chemical shifts | 28 | 27 | 96.4 |
15N chemical shifts | 3 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 5 | 0 | 0.0 |
1H chemical shifts | 6 | 6 | 100.0 |
15N chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 7 | 0 | 0.0 |
1H chemical shifts | 22 | 21 | 95.5 |
15N chemical shifts | 1 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 1 | 0 | 0.0 |
1H chemical shifts | 1 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG |||||||||||||||||||||||| ||||||||||||||| |||||| || ||||||||| | |||| | |||||||||||||||||||| ..AADLELERAADVKWEDQAEISGSS.ILSITISEDGSMSIK...EEQTLG...SG...EFAGVLWDV.S...VGKA.L.DGAYRIKQKGILGYSQIGAG -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI ||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||| ||| |||||| ||||| |||||||||||| |||| | VYKEGTFHTMWHVTRGAVLMHKGKRIE.SWADVKKDLISYGGGWKLEGEWKEGE.VQVLALE.GKN.RAVQTK.GLFKT.AGTIGAVSLDFS..TSGS.I -------210-------220-------230-------240 IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE ||||||||||||||||| |||||||||||||||||| ||| IDKKGKVVGLYGNGVVT.SGAYVSAIAQTEKSIEDN.EIE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG |||||||||||||| |||||| ||||||| ||||| | ||||| || ||| |||||||||| || |||| ...ADLELERAADVKWE..AEISGS..ILSITIS...SMSIK........G............VLWDV.....VG..ELE.GAYRIKQKGI..YS.IGAG --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI || ||||||| |||||||| ||| | || ||||| | | |||||| || ||| |||||| | |||| ||| | VY....FHTMWHV.RGAVLMHK..RIE..W.DV..DLISY...W.....W.....VQVLAL.....PR.VQT.PGLFKT....I.AVSL......SGS.I -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 -------210-------220-------230-------240 IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE || || ||||| ||| || |||||| ID..GK.VGLYG..VVT..GA.VSAIAQ -------210-------220--------
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSAADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLGGGGSGGGGEFAGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAG ||||||||||||||||||| |||||||||| |||||| ||||||| |||||||||| ||||||| ....DLELERAADVKWEDQAEIS.SSPILSITIS..GSMSIK......................LWDVPSP..........GAYRIKQKGI..YSQIGAG --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||| VYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTN.GTIGAVSLDFSPGTSGSPI -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 -------210-------220-------230-------240 IDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIE ||||||| |||||||||| |||||||||||||||||| IDKKGKV.GLYGNGVVTR.GAYVSAIAQTEKSIEDNP -------210-------220-------230-------