5PGM: Saccharomyces cerevisiae phosphoglycerate mutase

Saccharomyces cerevisiae phosphoglycerate mutase. Determined by X-ray diffraction at 2.12 Å resolution. Released 16 Feb 1999.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 16,692
Mol. weight: 221.77 kDa
Ligands: ALA
Released: 16 Feb 1999

Explore 5PGM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5PGM contains 147 α-helices and 104 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	11	1	11
α-helix	12-16	5
β-strand	18	1	12
β-strand	19	1	13
α-helix	25-26	2
β-strand	27	1	11
α-helix	28	1
α-helix	29-44	16
β-strand	51-54	4	10
α-helix	58-71	14
β-strand	78-80	3	10
α-helix	82-84	3
α-helix	86-88	3
α-helix	90-92	3
β-strand	93	1	13
β-strand	96	1	12
α-helix	97-114	18
α-helix	119-124	6
α-helix	135-137	3
α-helix	142-144	3
α-helix	151-161	11
α-helix	162-166	5
α-helix	167-171	5
α-helix	174-175	2
β-strand	176-180	5	10
α-helix	182-193	12
α-helix	199-202	4
β-strand	211-214	4	10
β-strand	215	1	14
β-strand	221	1	14
β-strand	226-227	2	10
α-helix	230-233	4

Chains B and H: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	15
β-strand	11	1	16
α-helix	12-15	4
β-strand	18	1	17
α-helix	25-26	2
β-strand	27	1	16
α-helix	28	1
α-helix	29-45	17
β-strand	51-54	4	15
α-helix	58-71	14
β-strand	78-80	3	15
α-helix	82-84	3
α-helix	86-88	3
α-helix	90-92	3
β-strand	96	1	17
α-helix	97-114	18
α-helix	119-124	6
α-helix	135-137	3
α-helix	142-144	3
α-helix	151-161	11
α-helix	162-166	5
α-helix	167-171	5
β-strand	176-180	5	15
α-helix	182-193	12
α-helix	199-201	3
β-strand	211-214	4	15
β-strand	215	1	18
β-strand	221	1	18
β-strand	226-227	2	15
α-helix	230-234	5

Chains C and F: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	11	1	7
α-helix	12-15	4
β-strand	18	1	8
α-helix	25-26	2
β-strand	27	1	7
α-helix	28	1
α-helix	29-45	17
β-strand	51-54	4	6
α-helix	58-71	14
β-strand	78-80	3	6
α-helix	82-84	3
α-helix	86-88	3
α-helix	90-92	3
β-strand	96	1	8
α-helix	97-104	8
α-helix	106-114	9
α-helix	119-124	6
α-helix	135-137	3
α-helix	151-161	11
α-helix	162-166	5
α-helix	167-171	5
β-strand	176-180	5	6
α-helix	182-193	12
β-strand	211-214	4	6
β-strand	215	1	9
β-strand	221	1	9
β-strand	226-227	2	6
α-helix	230-234	5

Chains D and E: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	11	1	2
α-helix	12-15	4
β-strand	18	1	3
β-strand	19	1	4
α-helix	25-26	2
β-strand	27	1	2
α-helix	28	1
α-helix	29-44	16
β-strand	51-54	4	1
α-helix	58-71	14
β-strand	78-80	3	1
α-helix	82-84	3
α-helix	86-88	3
α-helix	90-92	3
β-strand	93	1	4
β-strand	96	1	3
α-helix	97-104	8
α-helix	106-114	9
α-helix	119-124	6
α-helix	135-137	3
α-helix	151-161	11
α-helix	162-166	5
α-helix	167-171	5
α-helix	174-175	2
β-strand	176-180	5	1
α-helix	182-193	12
α-helix	200-202	3
β-strand	211-214	4	1
β-strand	215	1	5
β-strand	221	1	5
β-strand	226-227	2	1
α-helix	230-233	4

Chain G: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	28
β-strand	11	1	29
α-helix	12-16	5
β-strand	18	1	30
β-strand	19	1	31
α-helix	25-26	2
β-strand	27	1	29
α-helix	28	1
α-helix	29-44	16
β-strand	51-54	4	28
α-helix	58-71	14
β-strand	78-80	3	28
α-helix	82-84	3
α-helix	86-88	3
α-helix	90-92	3
β-strand	93	1	31
β-strand	96	1	30
α-helix	97-114	18
α-helix	119-124	6
α-helix	135-137	3
α-helix	142-144	3
α-helix	151-161	11
α-helix	162-166	5
α-helix	167-171	5
α-helix	174-175	2
β-strand	176-180	5	28
α-helix	182-193	12
α-helix	199-202	4
α-helix	210	1
β-strand	211-214	4	28
β-strand	215	1	32
β-strand	221	1	32
β-strand	226-227	2	28
α-helix	230-233	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphoglycerate mutase 1	A, B, C, D, E, F, G, H	protein	246	Saccharomyces cerevisiae	P00950 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>5PGM_1 PHOSPHOGLYCERATE MUTASE 1 (chains A, B, C, D, E, F, G, H)
PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRA
IQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPP
PPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAA
HGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAAGAAAV
ANQGKK

Ligands and cofactors

ID	Name	Formula	Copies
ALA	Alanine	C3 H7 N O2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. Rigden, D.J., Walter, R.A., Phillips, S.E. et al. J Mol Biol (1999) 286:1507-1517. DOI 10.1006/jmbi.1999.2566 · PubMed

Other PDB entries of the same protein (UniProt P00950 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QHF 1.7 Å, Yeast phosphoglycerate mutase-3PG complex structure to 1.7 a
4PGM 2.3 Å, Saccharomyces cerevisiae phosphoglycerate mutase
1BQ4 2.5 Å, Saccharomyces cerevisiae phosphoglycerate mutase in complex with benzene hexacarboxylate
1BQ3 2.7 Å, Saccharomyces cerevisiae phosphoglycerate mutase in complex with inositol hexakisphosphate
3PGM 2.8 Å, The structure of yeast phosphoglycerate mutase at 0.28 nm resolution

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