4pe4

Crystal Structure of Calcium-loaded S100B bound to SC1475

Method: X-RAY DIFFRACTION D_max: 59.8 Å Quality: GOOD

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

Protein S100-B

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–92 Chain X； UniProt 1–92	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

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 4PE4	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 construct Different mutation/modification 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 1–91（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 ligand/ion 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
1PSB Solution structure of calcium loaded S100B complexed to a peptide from N-Terminal regulatory domain of NDR kinase. Deposited 2003-06-21	Different construct Different oligomeric state 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 1–91（91 aa） Chain B 1–91（91 aa）	Not recorded	No recorded non-water small molecule	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
3CR2 X-ray structure of bovine Zn(2+),Ca(2+)-S100B Deposited 2008-04-04	Different construct Different mutation/modification Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
4PE7 Crystal Structure of Calcium-loaded S100B bound to SC1982 Deposited 2014-04-22	Different construct Different mutation/modification Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 1–92； UniProt 1–92 Author chain X； PDBConstruct 1–92； UniProt 1–92

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	4pe4
Deposition date deposition_date	2014-04-22
Structure title title	Crystal Structure of Calcium-loaded S100B bound to SC1475
Keywords keywords	malignant melanoma, calcium binding, complex, covalent inhibitor, METAL BINDING PROTEIN-INHIBITOR complex; METAL BINDING PROTEIN/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.48 Å
Radius of gyration Rg (electron density) rg_electron	17.15 Å
Forward intensity I(0) i0	8425060.00
Molecular weight molecular_weight	21480.0 kDa
Excluded volume excluded_volume	26836 Å³
Envelope volume envelope_volume	30746 Å³
Hydration-shell volume shell_volume	15373 Å³
Envelope diameter envelope_diameter	60.4 Å
Shell Rg shell_rg	22.78 Å
Envelope Rg envelope_rg	17.43 Å
Shape Rg shape_rg	17.15 Å
Total Rg total_rg	18.10 Å
Total atoms total_atoms	1500
Residues n_residues	180
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	59.8 Å
Rg (real space) rg_real	18.43 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	8.4250e+06
I(0) uncertainty (real space) i0_real_error	9.8110e+04
Rg (reciprocal space) rg_reciprocal	18.44 Å
I(0) (reciprocal space) i0_reciprocal	8425000.0000
Solution quality estimate total_estimate	0.8132
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.255
Kurtosis Kurtosis kurtosis	-0.396
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	909900.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; 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 (4)

Entity 1 Entity 1 polymer

Description description	Protein S100-B
Molecular weight formula_weight	10682.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,A
Atom count atom_count	1519

MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFEHE

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	2,3-dimethoxy-5-[(1S)-1-phenylpropyl]benzene-1,4-diol
Molecular weight formula_weight	288.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4pe4a_
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	d4pe4x_
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	4pe4A00
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	4pe4X00
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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Unit-cell length a length_a	35.015 Å
Unit-cell length b length_b	58.087 Å
Unit-cell length c length_c	47.891 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.178 Å
Low-resolution limit resolution_low	35.396 Å
R factor r_factor	0.2133
R_work r_work	0.2087
R_free r_free	0.2514

fit	/app/data/saxs_computation/pe/4pe4/4pe4.fit
pddf	/app/data/pr_computation/pe/4pe4/4pe4.pr.out
profile	/app/data/saxs_computation/pe/4pe4/4pe4.dat