1psb

Solution structure of calcium loaded S100B complexed to a peptide from N-Terminal regulatory domain of NDR kinase.

Method: SOLUTION NMR D_max: 53.6 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

S-100 protein, beta chain

Bos taurus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–91 Chain B； UniProt 1–91	Not recorded	Ndr Ser/Thr kinase-like protein × 2 （Q15208）	SOLUTION NMR NMR measurement conditions：pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.045 M/L；Pressure ambient NMR measurement conditions：pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.045 M/L；Pressure ambient NMR measurement conditions：pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.045 M/L；Pressure ambient NMR sample composition：1 mM 1H,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL \| 90% H2O/10% D2O NMR sample composition：1 mM 1H,13C,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL \| 90% H2O/10% D2O NMR sample composition：1 mM 1H,13C,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL \| 100% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1PSB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CFP S100B (S100BETA) NMR DATA WAS COLLECTED FROM A SAMPLE OF CALCIUM FREE PROTEIN AT PH 6.3 AND A TEMPERATURE OF 311 K AND 1.7-6.9 MM CONCENTRATION, 25 STRUCTURES Deposited 1996-06-04	Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–91（91 aa） Chain B 1–91（91 aa）	Mutation：N-TERMINAL METHIONINE REPLACES N-TERMINAL ACETYL GROUP OF THE NATURAL PROTEIN Mutation：N-TERMINAL METHIONINE REPLACES N-TERMINAL ACETYL GROUP OF THE NATURAL PROTEIN	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；314 K	Resolution not provided
1MHO THE 2.0 A STRUCTURE OF HOLO S100B FROM BOVINE BRAIN Deposited 1997-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–88（88 aa） Fragment：BETA CHAIN	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING-DROP VAPOR DIFFUSION METHOD, pH 8.0, vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.286
3CR2 X-ray structure of bovine Zn(2+),Ca(2+)-S100B Deposited 2008-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG3350, CaCl2, ZnCl2, Cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.88 Å R-free 0.268
3CR4 X-ray structure of bovine Pnt,Ca(2+)-S100B Deposited 2008-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 1–92（92 aa）	Not recorded	PNT 1,5-BIS(4-AMIDINOPHENOXY)PENTANE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；298 K；PEG3350, CaCl2, Penamidine, Cacodylate buffer, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.15 Å R-free 0.266
3CR5 X-ray structure of bovine Pnt-Zn(2+),Ca(2+)-S100B Deposited 2008-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 1–92（92 aa）	Not recorded	PNT 1,5-BIS(4-AMIDINOPHENOXY)PENTANE × 4 ZN ZINC ION × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；PEG3350, Pentamidine, CaCl2, ZnCl2, Cacodylate buffer, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.85 Å R-free 0.243
3GK1 X-ray structure of bovine SBi132,Ca(2+)-S100B Deposited 2009-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 32A 2-[(5-hex-1-yn-1-ylfuran-2-yl)carbonyl]-N-methylhydrazinecarbothioamide × 2 CAC CACODYLATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；28% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.10 Å R-free 0.257
3GK2 X-ray structure of bovine SBi279,Ca(2+)-S100B Deposited 2009-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 27A (Z)-2-[2-(4-methylpiperazin-1-yl)benzyl]diazenecarbothioamide × 2 CAC CACODYLATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；28% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.98 Å R-free 0.281
3GK4 X-ray structure of bovine SBi523,Ca(2+)-S100B Deposited 2009-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 53A ethyl 5-{[(1R)-1-(ethoxycarbonyl)-2-oxopropyl]sulfanyl}-1,2-dihydro[1,2,3]triazolo[1,5-a]quinazoline-3-carboxylate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；35% PEGMME550, 7.5mM CaCl2, 100mM Bis-Tris buffer, 2.5% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.90 Å R-free 0.228
3IQO 1.5 angstrom X-ray structure of bovine Ca(2+)-S100B Deposited 2009-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 6.3；295 K；25% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.3, sitting drop, temperature 295K	Resolution 1.50 Å R-free 0.242
3IQO 1.5 angstrom X-ray structure of bovine Ca(2+)-S100B Deposited 2009-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 6.3；295 K；25% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.3, sitting drop, temperature 295K	Resolution 1.50 Å R-free 0.242
3IQQ X-ray structure of bovine TRTK12-Ca(2+)-S100B Deposited 2009-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 6.8；295 K；26% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.8, sitting drop, temperature 295K	Resolution 2.01 Å R-free 0.266
3LK0 X-ray structure of bovine SC0067,Ca(2+)-S100B Deposited 2010-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa） Chain B 1–90（90 aa）	Not recorded	CA CALCIUM ION × 4 Z80 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；MPD, CaCl2, SC0067, Bis-Tris buffer, pH 7.0, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.04 Å R-free 0.291
3LK0 X-ray structure of bovine SC0067,Ca(2+)-S100B Deposited 2010-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–90（90 aa） Chain D 1–90（90 aa）	Not recorded	CA CALCIUM ION × 4 Z80 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；MPD, CaCl2, SC0067, Bis-Tris buffer, pH 7.0, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.04 Å R-free 0.291
3LK1 X-ray structure of bovine SC0322,Ca(2+)-S100B Deposited 2010-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa）	Not recorded	CA CALCIUM ION × 4 EMC ETHYL MERCURY ION × 2 JKE 2-sulfanylbenzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；PEGMME550, CaCl2, MgCl2, SC0322, HEPES buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.79 Å R-free 0.242
3LLE X-ray structure of bovine SC0322,Ca(2+)-S100B Deposited 2010-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa） Chain B 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 SGE 13-methyl-13,14-dihydro[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG3350, CaCl2, Li2SO4, Cacodylate buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.85 Å R-free 0.231
3LLE X-ray structure of bovine SC0322,Ca(2+)-S100B Deposited 2010-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–92（92 aa） Chain B 1–92（92 aa）	Not recorded	CA CALCIUM ION × 8 SGE 13-methyl-13,14-dihydro[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridine × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG3350, CaCl2, Li2SO4, Cacodylate buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.85 Å R-free 0.231
3RLZ 2.0 Angstrom X-ray structure of bovine Ca(2+)-S100B D63N Deposited 2011-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions SITTING DROP；pH 7；295 K；25% PEG3350, 7.5 mM calcium chloride, 100 mM cacodylate, SITTING DROP, temperature 295K	Resolution 2.01 Å R-free 0.259
3RLZ 2.0 Angstrom X-ray structure of bovine Ca(2+)-S100B D63N Deposited 2011-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions SITTING DROP；pH 7；295 K；25% PEG3350, 7.5 mM calcium chloride, 100 mM cacodylate, SITTING DROP, temperature 295K	Resolution 2.01 Å R-free 0.259
3RM1 1.24 Angstrom X-ray structure of bovine TRTK12-Ca(2+)-S100B D63N Deposited 2011-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions SITTING DROP；pH 6.875；295 K；22% PEG3350, 7.5 mM calcium chloride, 100 mM cacodylate, pH 6.875, SITTING DROP, temperature 295K	Resolution 1.24 Å R-free 0.223
4FQO Crystal Structure of Calcium-Loaded S100B Bound to SBi4211 Deposited 2012-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa）	Not recorded	CA CALCIUM ION × 4 AZ3 4,4'-[heptane-1,7-diylbis(oxy)]dibenzenecarboximidamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.21；295 K；PEG3350, sodium cacodylate, calcium chloride, pH 7.21, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.65 Å R-free 0.214
4PDZ Crystal Structure of Calcium-loaded S100B bound to SBi4172 Deposited 2014-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa） Chain B 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 CTI 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；20% 2-methyl-2,4-pentanediol, 0.1M Hepes, 7.5mM CaCl2	Resolution 1.73 Å R-free 0.268
4PE0 Crystal Structure of Calcium-loaded S100B bound to SBi4434 Deposited 2014-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa） Chain X 1–92（92 aa）	Not recorded	NQS 2-[(2-hydroxyethyl)sulfanyl]naphthalene-1,4-dione × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；40% 2-methyl-2,4-pentanediol, 0.1M Cacodylate, 7.5mM CaCl2, 4mM SBi4434	Resolution 1.08 Å R-free 0.211
4PE1 Crystal Structure of Calcium-loaded S100B bound to SC124 Deposited 2014-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa） Chain B 1–92（92 aa）	Not recorded	DCD DIETHYLCARBAMODITHIOIC ACID × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；40% 2-methyl-2,4-pentanediol, 0.1M Hepes,7.5mM CaCl2, 4mM SC124	Resolution 1.58 Å R-free 0.253
4PE4 Crystal Structure of Calcium-loaded S100B bound to SC1475 Deposited 2014-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa） Chain X 1–92（92 aa）	Not recorded	REV 2,3-dimethoxy-5-[(1S)-1-phenylpropyl]benzene-1,4-diol × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；40% 2-methyl-2,4-pentanediol, 0.1M Bis-Tris, 7.5mM CaCl2, 4mM SC1475	Resolution 2.18 Å R-free 0.251
4PE7 Crystal Structure of Calcium-loaded S100B bound to SC1982 Deposited 2014-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	ODN (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one × 2 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；40% 2-methyl-2,4-pentanediol, 0.1M Tris,7.5mM CaCl2, 4mM SC1982	Resolution 1.65 Å R-free 0.214
5DKN Crystal Structure of Calcium-loaded S100B bound to SBi4225 Deposited 2015-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 B7I 2,2'-[heptane-1,7-diylbis(oxybenzene-4,1-diyl)]bis(1H-imidazole) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；10% Peg 3,350; 0.1M Cacodylate, pH 6.4; 7.5mM CaCl2	Resolution 1.53 Å R-free 0.218
5DKQ Crystal Structure of Calcium-loaded S100B bound to SBi4214 Deposited 2015-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 5D0 2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；25% Peg 3,350; 0.1M Bis-Tris, pH 7.5; 7.5mM CaCl2; 5% glycerol	Resolution 1.59 Å R-free 0.230
5DKR Crystal Structure of Calcium-loaded S100B bound to SBi29 Deposited 2015-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa） Chain B 1–92（92 aa）	Not recorded	CA CALCIUM ION × 5 5CZ 2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-indole-6-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；40% 2-methyl-2,4-pentanediol; 0.1M Hepes, pH 7.0, 7.5mM CaCl2	Resolution 1.74 Å R-free 0.247
5ER4 Crystal Structure of Calcium-loaded S100B bound to SC0025 Deposited 2015-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 1–92（92 aa）	Not recorded	CA CALCIUM ION × 6 5RL 6-methyl-5,6,6~{a},7-tetrahydro-4~{H}-dibenzo[de,g]quinoline-10,11-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；25% polyethylene glycol monomethyl ether 550; 0.1M Hepes, pH8.0; 5% Glycerol; 7.5mM CaCl2	Resolution 1.81 Å R-free 0.224
5ER5 Crystal Structure of Calcium-loaded S100B bound to SC1990 Deposited 2015-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–92（92 aa）	Not recorded	CA CALCIUM ION × 4 ET ETHIDIUM × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；25% PEG 3,350; 0.1M Hepes, pH7.0; 5% Glycerol; 7.5mM CaCl2	Resolution 1.26 Å R-free 0.187
8FJ8 Crystal structure of Mn(2+),Ca(2+)-S100B Deposited 2022-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293.15 K；29% PEG MME 550, 100mM Cacodylate pH 6.9, 7.5mM CaCl2	Resolution 2.17 Å R-free 0.257

27 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S100B_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91 Author chain B； PDBConstruct 1–91； UniProt 1–91

Ndr Ser/Thr kinase-like protein

OrganismNot specified

UniProt Q15208

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 62–87 Chain D； UniProt 62–87	Fragment：N-terminal regulatory domain fragment, sequence database residue 60-85	S-100 protein, beta chain × 2 （P02638）	SOLUTION NMR NMR measurement conditions：pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.045 M/L；Pressure ambient NMR measurement conditions：pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.045 M/L；Pressure ambient NMR measurement conditions：pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.045 M/L；Pressure ambient NMR sample composition：1 mM 1H,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL \| 90% H2O/10% D2O NMR sample composition：1 mM 1H,13C,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL \| 90% H2O/10% D2O NMR sample composition：1 mM 1H,13C,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL \| 100% D2O	Resolution not provided

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1PSB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6BXI X-ray crystal structure of NDR1 kinase domain Deposited 2017-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 82–414（333 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4 M ammonium acetate, 0.1 M Bis-Tris propane pH 7	Resolution 2.20 Å R-free 0.212
6BXI X-ray crystal structure of NDR1 kinase domain Deposited 2017-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 82–414（333 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4 M ammonium acetate, 0.1 M Bis-Tris propane pH 7	Resolution 2.20 Å R-free 0.212

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STK38_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–26； UniProt 62–87 Author chain D； PDBConstruct 1–26； UniProt 62–87

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1psb
Deposition date deposition_date	2003-06-21
Structure title title	Solution structure of calcium loaded S100B complexed to a peptide from N-Terminal regulatory domain of NDR kinase.
Keywords keywords	HELIX-LOOP-HELIX, PROTEIN-PEPTIDE COMPLEX, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.41 Å
Radius of gyration Rg (electron density) rg_electron	20.01 Å
Forward intensity I(0) i0	4361580000.00
Molecular weight molecular_weight	550060.0 kDa
Excluded volume excluded_volume	683510 Å³
Envelope volume envelope_volume	81784 Å³
Hydration-shell volume shell_volume	26833 Å³
Envelope diameter envelope_diameter	103.3 Å
Shell Rg shell_rg	32.69 Å
Envelope Rg envelope_rg	27.92 Å
Shape Rg shape_rg	19.96 Å
Total Rg total_rg	20.30 Å
Total atoms total_atoms	76800
Residues n_residues	4680
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	53.6 Å
Rg (real space) rg_real	19.21 Å
Rg uncertainty (real space) rg_real_error	0.08 Å
I(0) (real space) i0_real	4.1440e+09
I(0) uncertainty (real space) i0_real_error	4.1320e+07
Rg (reciprocal space) rg_reciprocal	20.48 Å
I(0) (reciprocal space) i0_reciprocal	4362000000.0000
Solution quality estimate total_estimate	0.6859
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	3.5170
Highest regularization parameter α highest_alpha	875700.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.996; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1psba_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

Domain ID domain_id	d1psbb_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

CATH v4.4 (2 domains)

Domain ID domain_id	1psbA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1psbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Description description	S-100 protein, beta chain
Molecular weight formula_weight	10550.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	76800

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Description description	Ndr Ser/Thr kinase-like protein
Molecular weight formula_weight	3232.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

Solution structure of calcium loaded S100B complexed to a peptide from N-Terminal regulatory domain of NDR kinase.

1. Protein Identity and Related Structures Protein Identity & Related Structures

S-100 protein, beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Ndr Ser/Thr kinase-like protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ps/1psb/1psb.fit
pddf	/app/data/pr_computation/ps/1psb/1psb.pr.out
profile	/app/data/saxs_computation/ps/1psb/1psb.dat