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Saccharomyces cerevisiae phosphoglycerate mutase

Analyse Saccharomyces cerevisiae phosphoglycerate mutase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5PGM
Type: protein
Length: 1,877 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglycerate mutase 1
EC: 5.4.2.1
UniProt: P00950
Ligands: ALA, SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, B, F, H	Phosphoglycerate mutase 1 (EC 5.4.2.1)	protein	235	43% helix, 14% strand	P00950
A, E, G	Phosphoglycerate mutase 1 (EC 5.4.2.1)	protein	234	45% helix, 14% strand	P00950

Ligands and binding sites

ALA · Alanine · ligand · chains E
SO4 · Sulfate ion · ion · 16 copies · chains D, C, A, B, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.77	0.82	61	empty
2	589	0.76	0.83	60	empty
3	430	0.75	0.84	55	empty
4	438	0.75	0.84	52	empty
5	591	0.75	0.81	56	empty

Interfaces

13 interfaces between chains.

A–B · 979 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 977 Å² buried · 9 hydrogen bonds · protein-protein
D–C · 977 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 975 Å² buried · 15 hydrogen bonds · protein-protein
C–A · 912 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5PGM · Saccharomyces cerevisiae phosphoglycerate mutase · the same entry in another collection · chain C against C, TM-score 1.00
P00950 · AlphaFold monomer V2.0 prediction for phosphoglycerate mutase 1 (P00950) · a predicted model of the same protein · chain F against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00950
Elsewhere: RCSB PDB 5PGM · PDBe 5PGM · UniProt P00950

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