5y2u

X-ray structure of Phosphoglycerate Mutase 1(PGAM1) complexed with a small molecule

Method: X-RAY DIFFRACTION D_max: 86.5 Å Quality: GOOD

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

Phosphoglycerate mutase 1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–254 Chain C； UniProt 1–254	Not recorded	CL CHLORIDE ION × 1 AZN ALIZARIN RED × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；8% PEG3350 100mM MES 6.0	Resolution 1.98 Å R-free 0.226

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 5Y2U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YFK Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–253（254 aa） Chain B 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, (NH4)2SO4, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.70 Å R-free 0.255
1YJX Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 0–253（254 aa） Chain B 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.80 Å R-free 0.272
1YJX Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 0–253（254 aa） Chain D 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.80 Å R-free 0.272
1YJX Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 0–253（254 aa） Chain F 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.80 Å R-free 0.272
1YJX Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 0–253（254 aa） Chain H 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.80 Å R-free 0.272
1YJX Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 0–253（254 aa） Chain J 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.80 Å R-free 0.272
1YJX Crystal structure of human B type phosphoglycerate mutase Deposited 2005-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 0–253（254 aa） Chain L 0–253（254 aa）	Not recorded	CL CHLORIDE ION × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；297 K；PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.80 Å R-free 0.272
22RB Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2026-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	GOL GLYCEROL × 8 CL CHLORIDE ION × 1 A1E4N 4-(4-chlorophenyl)-2-[[4-(3,6-dihydro-2~{H}-pyran-4-yl)phenyl]sulfonylamino]benzoic acid × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289.15 K；1 mM MES 6.0, 8% PEG 3350	Resolution 1.75 Å R-free 0.205
22RH Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2026-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	A1E4P 5-chloranyl-3-methyl-1~{H}-indole-2-carboxylic acid × 3 GOL GLYCEROL × 5 CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289.15 K；100 mM MES 6.0, 8% PEG3350	Resolution 2.28 Å R-free 0.234
22RL Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2026-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	A1E4O 7-bromanyl-5-chloranyl-3-(2-hydroxyethylamino)-1-benzothiophene-2-carboxylic acid × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289.15 K；100 mM MES 6.0, 8% PEG3350	Resolution 3.19 Å R-free 0.264
22TN Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2026-01-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	GOL GLYCEROL × 6 CL CHLORIDE ION × 1 A1E4Q ~{N}-[5-(4-chlorophenyl)-2-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]-4-phenyl-benzenesulfonamide × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；100 mM MES 6.0, 8% PEG3350	Resolution 2.03 Å R-free 0.226
22WM Phosphoglycerate mutase 1 complexed with a fragment Deposited 2026-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	A1E4R 4-(4-chlorophenyl)benzoic acid × 2 GOL GLYCEROL × 10 CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289.15 K；1 mM MES 6.0, 8% PEG3350	Resolution 1.91 Å R-free 0.229
4GPI Crystal structure of human B type phosphoglycerate mutase Deposited 2012-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 8% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.08 Å R-free 0.233
4GPZ Crystal structure of human B type phosphoglycerate mutase H11 phosphorylated form Deposited 2012-08-22	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 1–254（254 aa） Fragment：Human type B phosphoglycerate mutase Chain B 1–254（254 aa） Fragment：Human type B phosphoglycerate mutase	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.214
5Y2I Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A Deposited 2017-07-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	8KX 3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)-~{N}-[4-(trifluoromethyl)phenyl]anthracene-2-sulfonamide × 1 CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, MES	Resolution 1.92 Å R-free 0.214
5Y35 Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH1 Deposited 2017-07-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 8LF ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-methyl-benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES, pH 6.0, PEG3350	Resolution 1.99 Å R-free 0.244
5Y64 Phosphoglycerate mutase 1 H11 phosphorylated form complexed with KH1 Deposited 2017-08-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 8LF ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-methyl-benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；MES, PEG3350	Resolution 2.15 Å R-free 0.236
5Y65 Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2 Deposited 2017-08-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 HKB ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-(dimethylamino)benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES pH 6.0, 8%PEG3350	Resolution 2.55 Å R-free 0.248
5ZRM Phosphoglycerate mutase 1 complexed with a small molecule inhibitor In-AC Deposited 2018-04-24	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 B 2–235（234 aa） Fragment：UNP residues 2-235 Chain C 2–235（234 aa） Fragment：UNP residues 2-235	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 9HU 2-[(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)sulfamoyl]phenyl acetate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES, pH 6.0, PEG3350	Resolution 2.28 Å R-free 0.232
5ZS7 Acetylation of lysine 100 in Phosphoglycerate mutase 1 Deposited 2018-04-28	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 B 3–235（233 aa） Chain C 2–235（234 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES, pH 6.0, PEG 3350	Resolution 2.68 Å R-free 0.255
5ZS8 Acetylation of lysine 100 of Phosphoglycerate mutase 1 complexed with KH_ol Deposited 2018-04-28	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 B 2–235（234 aa） Chain C 2–241（240 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 9JF N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)-2-hydroxybenzene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES, pH 6.0, PEG 3350	Resolution 2.20 Å R-free 0.220
6ISN Phosphoglycerate mutase 1 complexed with a small molecule inhibitor Deposited 2018-11-17	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 B 2–235（234 aa） Fragment：UNP residues 2-235 Chain C 2–235（234 aa） Fragment：UNP residues 2-235	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 AW6 4-chloro-N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)benzene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES, pH 6.0, PEG3350	Resolution 1.98 Å R-free 0.225
7XB7 Phosphoglycerate mutase 1 complexed with a covalent inhibitor Deposited 2022-03-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 CKF 3-[[5-(cyclopenten-1-yl)-2-(methylcarbamoyl)phenyl]sulfamoyl]benzenesulfonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；MES, pH 6.0, PEG3350	Resolution 2.20 Å R-free 0.236
7XB8 Phosphoglycerate mutase 1 complexed with a covalent inhibitor Deposited 2022-03-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 H6I 4-(cyclopenten-1-yl)-2-[(3-sulfophenyl)sulfonylamino]benzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG3350, 100mM MES 6.0	Resolution 1.60 Å R-free 0.191
7XB9 Phosphoglycerate mutase 1 complexed with a covalent inhibitor Deposited 2022-03-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 H5X 3-[[5-(cyclopenten-1-yl)-2-methoxycarbonyl-phenyl]sulfamoyl]benzenesulfonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 1.58 Å R-free 0.196
8IT4 Phosphoglycerate mutase 1 complexed with a covalent inhibitor Deposited 2023-03-22	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 1–254（254 aa） Chain B 1–254（254 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 SKU 3-[[5-(4-chlorophenyl)-2-methoxycarbonyl-thiophen-3-yl]sulfamoyl]benzenesulfonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES6.0	Resolution 2.40 Å R-free 0.230
8IT5 Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 QAI 5-(4-chlorophenyl)-3-[(4-phenylphenyl)sulfonylamino]thiophene-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 2.20 Å R-free 0.229
8IT6 Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 Q90 4-[4-chloranyl-2-(2-hydroxy-2-oxoethyloxy)phenyl]-2-[(4-phenylphenyl)sulfonylamino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 2.55 Å R-free 0.267
8IT7 Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 Q9F 4-(4-chlorophenyl)-2-oxidanyl-6-[(4-phenylphenyl)sulfonylamino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 2.80 Å R-free 0.249
8IT8 Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 Q9L 4-(4-chlorophenyl)-2-[(4-phenylphenyl)sulfonylamino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 1.95 Å R-free 0.209
8ITB Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 Q9R 5-(3-chloranyl-4-fluoranyl-phenyl)-2-oxidanyl-3-[(4-phenylphenyl)sulfonylamino]benzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 2.38 Å R-free 0.243
8ITC Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 QA0 5-(4-chlorophenyl)-3-[(4-phenylphenyl)sulfonylamino]phthalic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 1.88 Å R-free 0.220
8ITD Phosphoglycerate mutase 1 complexed with a compound Deposited 2023-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 QA3 4-(4-chloranyl-2-oxidanyl-phenyl)-2-[(4-phenylphenyl)sulfonylamino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG3350, 100mM MES 6.0	Resolution 1.90 Å R-free 0.197
9LG2 Phosphoglycerate mutase 1 complexed with a covalent inhibitor Deposited 2025-01-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.2 MAmmonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000	Resolution 2.02 Å R-free 0.229
9XVS Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2025-11-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	A1E1K 6-chloranyl-10-oxidanylidene-1,9-diazatricyclo[6.4.1.0^{4,13}]trideca-2,4(13),5,7-tetraene-2-carboxylic acid × 2 GOL GLYCEROL × 8 CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；100 mM MES 6.0, 8% PEG3350	Resolution 2.08 Å R-free 0.240
9XW4 Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2025-11-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	A1E1J 7-bromanyl-5-chloranyl-3-phenylazanyl-1-benzothiophene-2-carboxylic acid × 3 GOL GLYCEROL × 5 CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；100 mM MES 6.0, 8% PEG3350	Resolution 2.11 Å R-free 0.209
9XWT Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor Deposited 2025-11-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–254（254 aa） Chain C 1–254（254 aa）	Not recorded	A1E1M 7-bromanyl-5-chloranyl-1~{H}-indole-2-carboxylic acid × 3 GOL GLYCEROL × 3 CL CHLORIDE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；100 mM MES 6.0, 8% PEG3350	Resolution 2.28 Å R-free 0.249

32 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PGAM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–254； UniProt 1–254 Author chain C； PDBConstruct 1–254； UniProt 1–254

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	5y2u
Deposition date deposition_date	2017-07-27
Structure title title	X-ray structure of Phosphoglycerate Mutase 1(PGAM1) complexed with a small molecule
Keywords keywords	Phosphoglycerate Mutase 1, ISOMERASE-INHIBITOR complex; ISOMERASE/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	25.44 Å
Radius of gyration Rg (electron density) rg_electron	24.60 Å
Forward intensity I(0) i0	49277000.00
Molecular weight molecular_weight	54507.0 kDa
Excluded volume excluded_volume	68198 Å³
Envelope volume envelope_volume	81301 Å³
Hydration-shell volume shell_volume	27714 Å³
Envelope diameter envelope_diameter	89.9 Å
Shell Rg shell_rg	31.71 Å
Envelope Rg envelope_rg	24.91 Å
Shape Rg shape_rg	24.59 Å
Total Rg total_rg	25.44 Å
Total atoms total_atoms	3846
Residues n_residues	471
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	86.5 Å
Rg (real space) rg_real	25.47 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	4.9280e+07
I(0) uncertainty (real space) i0_real_error	7.0520e+05
Rg (reciprocal space) rg_reciprocal	25.46 Å
I(0) (reciprocal space) i0_reciprocal	49280000.0000
Solution quality estimate total_estimate	0.8750
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.420
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14040000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.986

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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	Phosphoglycerate mutase 1
Molecular weight formula_weight	29917.1 kDa
EC 编号 ec_number	5.4.2.11,5.4.2.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C
Atom count atom_count	4055

MAAYKLVLIRHGESAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAKKLEHHHHHH

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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ALIZARIN RED
Molecular weight formula_weight	320.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5y2ub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

Domain ID domain_id	d5y2uc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.1 — Cofactor-dependent phosphoglycerate mutase

CATH v4.4 (2 domains)

Domain ID domain_id	5y2uB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	5y2uC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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8. Citations (1)

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Unit-cell length a length_a	82.640 Å
Unit-cell length b length_b	85.267 Å
Unit-cell length c length_c	102.466 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	43.544 Å
R factor r_factor	0.2011
R_work r_work	0.1997
R_free r_free	0.2260

fit	/app/data/saxs_computation/y2/5y2u/5y2u.fit
pddf	/app/data/pr_computation/y2/5y2u/5y2u.pr.out
profile	/app/data/saxs_computation/y2/5y2u/5y2u.dat