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Crystal structure of the R515L missense variant of human PGM1

Analyse Crystal structure of the R515L missense variant of human PGM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VEC
Type: protein
Length: 1,128 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglucomutase-1
EC: 5.4.2.2
UniProt: P36871
Ligands: MG, SO4
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphoglucomutase-1 (EC 5.4.2.2)	protein	564	36% helix, 25% strand	P36871

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1076	0.76	0.79	101	SO4, GOL
2	756	0.71	0.78	64	SO4
3	224	0.56	0.79	41	SO4
4	161	0.45	0.75	24	empty
5	98	0.37	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 305 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5VEC · Crystal Structure of the R515L missense variant of human PGM1 · the same entry in another collection · chain A against A, TM-score 1.00
P36871 · AlphaFold monomer V2.0 prediction for phosphoglucomutase-1 (P36871) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P36871
Elsewhere: RCSB PDB 5VEC · PDBe 5VEC · UniProt P36871

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