Siderocalin Q83 reveals a dual ligand binding mode
MTVPDRSEIA GKWYVVALAS NTEFFLREKD KMKMAMARIS FLGEDELKVS YAVPKPNGCR KWETTFKKTS DDGEVYYSEE AKKKVEVLDT DYKSYAVIYA TRVKDGRTLH MMRLYSRSPE VSPAATAIFR KLAGERNYTD EMVAMLPRQE ECTVDEV
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS59:SG | 1:CYS152:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 73.5 % (1359 of 1850) | 61.1 % (590 of 965) | 84.8 % (617 of 728) | 96.8 % (152 of 157) |
Backbone | 95.2 % (885 of 930) | 93.3 % (293 of 314) | 95.7 % (445 of 465) | 97.4 % (147 of 151) |
Sidechain | 57.9 % (620 of 1071) | 45.6 % (297 of 651) | 76.8 % (318 of 414) | 83.3 % (5 of 6) |
Aromatic | 18.0 % (27 of 150) | 10.7 % (8 of 75) | 23.3 % (17 of 73) | 100.0 % (2 of 2) |
Methyl | 92.4 % (146 of 158) | 89.9 % (71 of 79) | 94.9 % (75 of 79) |
1. Q83
MTVPDRSEIA GKWYVVALAS NTEFFLREKD KMKMAMARIS FLGEDELKVS YAVPKPNGCR KWETTFKKTS DDGEVYYSEE AKKKVEVLDT DYKSYAVIYA TRVKDGRTLH MMRLYSRSPE VSPAATAIFR KLAGERNYTD EMVAMLPRQE ECTVDEVSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | TMP | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | TMP | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | TMP | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | TMP | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | TMP | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Varian INOVA - 800 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Q83 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | EB4 | natural abundance | 1 mM | |
3 | Gallium(III) | natural abundance | 1 mM | |
4 | ARACHIDONIC ACID | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 50 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_17577_2lbv.nef |
Input source #2: Coordindates | 2lbv.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) |
---|---|---|---|---|
A:59:CYS:SG | A:152:CYS:SG | unknown | oxidized 98.6%, reduced 1.4%, CA 54.0, CB 34.9 ppm | 2.02 |
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) |
---|---|---|---|---|
2:1:EB4:O5 | 3:1:GA:GA | unknown | unknown | n/a |
2:1:EB4:O3 | 3:1:GA:GA | unknown | unknown | n/a |
2:1:EB4:O1 | 3:1:GA:GA | unknown | unknown | n/a |
2:1:EB4:O4 | 3:1:GA:GA | unknown | unknown | n/a |
2:1:EB4:O6 | 3:1:GA:GA | unknown | unknown | n/a |
2:1:EB4:O2 | 3:1:GA:GA | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | GA | GALLIUM (III) ION | None |
C | 1 | EB4 | N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) | Distance restraints |
D | 1 | ACD | ARACHIDONIC ACID | None |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 157 | 0 | 0 | 100.0 |
Content subtype: combined_17577_2lbv.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ...PDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNG.RKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV |||| |||||||||||||||||||||||||||||||||||||||||||||||||||| TRVK.GRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 728 | 613 | 84.2 |
1H chemical shifts | 965 | 558 | 57.8 |
15N chemical shifts | 168 | 151 | 89.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 314 | 296 | 94.3 |
1H chemical shifts | 314 | 294 | 93.6 |
15N chemical shifts | 151 | 146 | 96.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 414 | 317 | 76.6 |
1H chemical shifts | 651 | 264 | 40.6 |
15N chemical shifts | 17 | 5 | 29.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 87 | 82 | 94.3 |
1H chemical shifts | 87 | 80 | 92.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 73 | 17 | 23.3 |
1H chemical shifts | 75 | 8 | 10.7 |
15N chemical shifts | 2 | 2 | 100.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA |||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||| |||||| ......SEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNG.R.WETTFKKTSDDGEVYYSEEAKKKVEVLDTDYK.YAVIYA -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV |||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||| TRVK.GRTLH.MRLYSRSPEVS.AATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ......SEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV |||| ||||||||||||||||| |||||||||||||||||||||||||||||||||| TRVK.GRTLHMMRLYSRSPEVS.AATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV
- X | X
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA ||| |||| |||||||| | |||| | | |||||||| | | | || ||| ||||| | | ||||||| ............WYV.ALAS..EFFLREKD.M..AMAR.S.L...ELKVSYAV......R.W.T.FK........YYS...KKKVE..D.D..SYAVIYA --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV |||| | | ||||||| |||||||||||||| | | TRVK..R.L.MMRLYSR.....PAATAIFRKLAGER.....M.A -------110-------120-------130-------140----
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||| ....DRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVP.PNGCRKWETTFKK....GEVYYSEEAKKKVEVLDTDYKSYAVIYA --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV ||||||||||||||||| ||||||||||||||||||||||||||||||||||||| TRVKDGRTLHMMRLYSR..EVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDE -------110-------120-------130-------140-------150------
RDC restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYA |||| ||| |||||||||||||||||||||||||| ||||||| |||| ||||||| ||||||| |||||||||||| |||||| .......EIAG.WYV.ALASNTEFFLREKDKMKMAMARISFL....LKVSYAV.......KWET.FKKTSDD.EVYYSEE.KKKVEVLDTDYK.YAVIYA --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150------- TRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDEMVAMLPRQEECTVDEV |||| ||||||||||||| | ||||||||| ||||| ||||||| | ||||| TRVK.GRTLHMMRLYSRS...S.AATAIFRKL.GERNY.DEMVAML.R.EECTV -------110-------120-------130-------140-------150----