3m0w

Structure of S100A4 with PCP

Method: X-RAY DIFFRACTION D_max: 97.2 Å Quality: EXCELLENT

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

Protein S100-A4

Homo sapiens

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 2–101 Chain B； UniProt 2–101 Chain C； UniProt 2–101 Chain D； UniProt 2–101 Chain E； UniProt 2–101 Chain F； UniProt 2–101 Chain G； UniProt 2–101 Chain H； UniProt 2–101 Chain I； UniProt 2–101 Chain J； UniProt 2–101	Not recorded	P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 12 CA CALCIUM ION × 20 DIO 1,4-DIETHYLENE DIOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.80 Å R-free 0.302
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–101 Chain B； UniProt 2–101	Not recorded	P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 3 CA CALCIUM ION × 4 DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.80 Å R-free 0.302
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–101 Chain D； UniProt 2–101	Not recorded	P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.80 Å R-free 0.302
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2–101 Chain F； UniProt 2–101	Not recorded	P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.80 Å R-free 0.302
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 2–101 Chain H； UniProt 2–101	Not recorded	P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.80 Å R-free 0.302
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 2–101 Chain J； UniProt 2–101	Not recorded	P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 3 CA CALCIUM ION × 4 DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.80 Å R-free 0.302

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 3M0W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M31 Three-Dimensional Solution Structure of Apo-Mts1 Deposited 2002-06-26	Different construct 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 1–101（101 aa） Chain B 1–101（101 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25mM；Pressure ambient NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25mM；Pressure ambient NMR sample composition 3mM Mts1, U-15N, 16mM D11-Tris, 2mM EGTA, 0.3mM NAN3, 8mM NaCl, 6mM DTT \| 93% H2O/7% D2O NMR sample composition 3mM Mts1, U-13C,15N, 16mM D11-Tris, 2mM EGTA, 0.3mM NAN3, 8mM NaCl, 6mM DTT \| 93% H2O/7% D2O	Resolution not provided
2LNK Solution structure of Ca-bound S100A4 in complex with non-muscle myosin IIA Deposited 2011-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–101（101 aa） Chain B 1–101（101 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；313 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 0.5 mM protein_1, 1 mM [U-100% 13C; U-100% 15N] protein_2, 5 mM CALCIUM ION, 20 mM MES, 20 mM sodium chloride, 4 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MRD Solution structure of human Ca2+-loaded S100A4 cys-free mutant Deposited 2014-07-03	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 1–101（101 aa） Chain B 1–101（101 aa）	Mutation：C3S,C76S,C81S,C86S Mutation：C3S,C76S,C81S,C86S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] S100A4-1, 16 mM TRIS-2, 8 mM sodium chloride-3, 6 mM calcium chloride-4, 0.1 mM EDTA-5, 0.34 mM sodium azide-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2Q91 Structure of the Ca2+-Bound Activated Form of the S100A4 Metastasis Factor Deposited 2007-06-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–101（101 aa） Chain B 1–101（101 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.05M ammonium sulfate, 0.05M Bis-Tris, 27.5% pentaethythritol-pthoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.63 Å R-free 0.217
3C1V The 1.5 A Crystal structure of Ca2+-bound S100A4 Deposited 2008-01-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–101（101 aa） Chain B 1–101（101 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；40% PEG600, 0.1M CHES, pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.50 Å R-free 0.218
3C1V The 1.5 A Crystal structure of Ca2+-bound S100A4 Deposited 2008-01-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–101（101 aa） Chain D 1–101（101 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；40% PEG600, 0.1M CHES, pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.50 Å R-free 0.218
3CGA Crystal structure of metastasis-associated protein S100A4 in the active, calcium-bound form Deposited 2008-03-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–101（101 aa） Chain B 1–101（101 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；298 K；20% (w/v) PEG 3350 and 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50	Resolution 2.03 Å R-free 0.331
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–101（101 aa） Chain B 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain S 1–101（101 aa） Chain T 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–101（101 aa） Chain D 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–101（101 aa） Chain F 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–101（101 aa） Chain H 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 1–101（101 aa） Chain J 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 1–101（101 aa） Chain L 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 1–101（101 aa） Chain N 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–101（101 aa） Chain P 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Q 1–101（101 aa） Chain R 1–101（101 aa）	Not recorded	TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.259
3ZWH Ca2+-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with myosin IIA Deposited 2011-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–101（101 aa） Chain B 1–101（101 aa）	Mutation：YES Mutation：YES	CA CALCIUM ION × 4 ACT ACETATE ION × 2 AZI AZIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；30% PEG 4000, 0.2 M NA-ACETATE PH 5.6, 0.1 M NA-CITRATE.	Resolution 1.94 Å R-free 0.206
4CFQ Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA Deposited 2013-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–88（88 aa） Fragment：RESIDUES 1-88 Chain D 1–88（88 aa） Fragment：RESIDUES 1-88	Mutation：YES Mutation：YES	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1 M MIB, PH 4, 25% W/V PEG 1500	Resolution 1.37 Å R-free 0.193
4CFQ Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA Deposited 2013-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–88（88 aa） Fragment：RESIDUES 1-88 Chain B 1–88（88 aa） Fragment：RESIDUES 1-88	Mutation：YES Mutation：YES	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1 M MIB, PH 4, 25% W/V PEG 1500	Resolution 1.37 Å R-free 0.193
4CFR Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA Deposited 2013-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–101（101 aa） Fragment：RESDIUES 1-101 Chain B 1–101（101 aa） Fragment：RESDIUES 1-101	Mutation：YES Mutation：YES	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% W/V PEG 4000	Resolution 1.40 Å R-free 0.175
4ETO Structure of S100A4 in complex with non-muscle myosin-IIA peptide Deposited 2012-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–93（93 aa） Fragment：UNP residues 1-93 Chain B 1–93（93 aa） Fragment：UNP residues 1-93	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, 30% (v/v) Jeffamine ED-2001, Vapor diffusion, Sitting drop, temperature 298K	Resolution 1.54 Å R-free 0.251
4HSZ Structure of truncated (delta8C) S100A4 Deposited 2012-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–93（93 aa） Fragment：UNP residues 1-93 Chain B 1–93（93 aa） Fragment：UNP residues 1-93	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.25 Å R-free 0.277
4HSZ Structure of truncated (delta8C) S100A4 Deposited 2012-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–93（93 aa） Fragment：UNP residues 1-93 Chain D 1–93（93 aa） Fragment：UNP residues 1-93	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.25 Å R-free 0.277
5LPU Crystal structure of Annexin A2 complexed with S100A4 Deposited 2016-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–101（101 aa） Chain D 1–101（101 aa）	Not recorded	CA CALCIUM ION × 14 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.1M Bis Tris pH 6.5, 0.2M ammonium acetate 4% PEG4000 and 1,5% glycerol	Resolution 2.10 Å R-free 0.207
6T58 Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone Deposited 2019-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–93（93 aa） Chain A 2–93（92 aa）	Mutation：A280E,A280E,A280E,A280E Mutation：A280E,A280E,A280E,A280E	GOL GLYCEROL × 2 CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.12 M Alcohols 0.1 M Sodium HEPES; MOPS (acid) pH7.5 20% v/v Ethylene glycol; 10 % w/v PEG 8000 Morpheus D6	Resolution 3.10 Å R-free 0.272
6T58 Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone Deposited 2019-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–93（93 aa） Chain B 2–93（92 aa）	Mutation：A280E,A280E,A280E,A280E Mutation：A280E,A280E,A280E,A280E	GOL GLYCEROL × 2 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.12 M Alcohols 0.1 M Sodium HEPES; MOPS (acid) pH7.5 20% v/v Ethylene glycol; 10 % w/v PEG 8000 Morpheus D6	Resolution 3.10 Å R-free 0.272
7PSP Crystal structure of S100A4 labeled with NU000846b. Deposited 2021-09-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–100（100 aa） Chain B 1–100（100 aa）	Not recorded	85Q (2R,4R)-1-(2-chloranylethanoyl)-N-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Labelled protein in 3M sodium chloride, 0.1M citrate, pH 3.5	Resolution 2.61 Å R-free 0.286
7PSQ Crystal structure of S100A4 labeled with NU074381b. Deposited 2021-09-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–100（100 aa） Chain E 1–100（100 aa）	Not recorded	CA CALCIUM ION × 4 EDO 1,2-ETHANEDIOL × 1 82Q (2~{R},4~{R})-1-ethanoyl-~{N}-naphthalen-1-yl-4-phenyl-pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；MES 25mM, 12.5% ethylene glycol	Resolution 1.91 Å R-free 0.236
7PSQ Crystal structure of S100A4 labeled with NU074381b. Deposited 2021-09-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–100（100 aa） Chain G 1–100（100 aa）	Not recorded	CA CALCIUM ION × 5 EDO 1,2-ETHANEDIOL × 2 82Q (2~{R},4~{R})-1-ethanoyl-~{N}-naphthalen-1-yl-4-phenyl-pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；MES 25mM, 12.5% ethylene glycol	Resolution 1.91 Å R-free 0.236

16 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S10A4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 2–101 Author chain B； PDBConstruct 1–100； UniProt 2–101 Author chain C； PDBConstruct 1–100； UniProt 2–101 Author chain D； PDBConstruct 1–100； UniProt 2–101 Author chain E； PDBConstruct 1–100； UniProt 2–101 Author chain F； PDBConstruct 1–100； UniProt 2–101 Author chain G； PDBConstruct 1–100； UniProt 2–101 Author chain H； PDBConstruct 1–100； UniProt 2–101 Author chain I； PDBConstruct 1–100； UniProt 2–101 Author chain J； PDBConstruct 1–100； UniProt 2–101

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	3m0w
Deposition date deposition_date	2010-03-03
Structure title title	Structure of S100A4 with PCP
Keywords keywords	MTS1, S100 CALCIUM-BINDING PROTEIN A4, S100A4, METASTASIN, Calcium Binding Protein; Calcium Binding Protein
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	34.11 Å
Radius of gyration Rg (electron density) rg_electron	32.41 Å
Forward intensity I(0) i0	174237000.00
Molecular weight molecular_weight	105720.0 kDa
Excluded volume excluded_volume	132120 Å³
Envelope volume envelope_volume	180250 Å³
Hydration-shell volume shell_volume	44481 Å³
Envelope diameter envelope_diameter	97.9 Å
Shell Rg shell_rg	41.24 Å
Envelope Rg envelope_rg	31.18 Å
Shape Rg shape_rg	32.42 Å
Total Rg total_rg	33.16 Å
Total atoms total_atoms	7342
Residues n_residues	891
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	97.2 Å
Rg (real space) rg_real	33.85 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.7420e+08
I(0) uncertainty (real space) i0_real_error	2.6690e+06
Rg (reciprocal space) rg_reciprocal	34.01 Å
I(0) (reciprocal space) i0_reciprocal	174300000.0000
Solution quality estimate total_estimate	0.9066
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.7 Å
Skewness Skewness skewness	-0.120
Kurtosis Kurtosis kurtosis	-0.701
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17620000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein S100-A4
Molecular weight formula_weight	11614.3 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	7351

ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPRKK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine
Molecular weight formula_weight	373.9 kDa
Source method src_method	syn
Copy count entity_count	12

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	20

Entity 4 Entity 4 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3m0wa_
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	d3m0wb_
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	d3m0wc_
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	d3m0wd_
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	d3m0we_
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	d3m0wf_
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	d3m0wg_
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	d3m0wh_
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	d3m0wi_
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	d3m0wj_
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 (10 domains)

Domain ID domain_id	3m0wA00
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	3m0wB00
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	3m0wC00
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	3m0wD00
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	3m0wE00
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	3m0wF00
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	3m0wG00
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	3m0wH00
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	3m0wI00
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	3m0wJ00
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	54.577 Å
Unit-cell length b length_b	102.275 Å
Unit-cell length c length_c	117.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	24.980 Å
R factor r_factor	0.2540
R_work r_work	0.2520
R_free r_free	0.3020

fit	/app/data/saxs_computation/m0/3m0w/3m0w.fit
pddf	/app/data/pr_computation/m0/3m0w/3m0w.pr.out
profile	/app/data/saxs_computation/m0/3m0w/3m0w.dat