Research workbench

Crystal structure of H105A PGAM5 dimer

Analyse Crystal structure of H105A PGAM5 dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CNI
Type: protein
Length: 373 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial
EC: 3.1.3.16
UniProt: Q96HS1
Ligands: NA, PO4
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	191	39% helix, 21% strand	Q96HS1
B	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	182	41% helix, 22% strand	Q96HS1

Ligands and binding sites

NA · Sodium ion · metal · 6 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	146	0.59	0.83	19	empty
2	172	0.58	0.81	21	empty
3	56	0.43	0.82	11	empty
4	104	0.36	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 1143 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

6CNI · Crystal structure of H105A PGAM5 dimer · the same entry in another collection · chain A against A, TM-score 1.00
Q96HS1 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PGAM5… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q96HS1
Elsewhere: RCSB PDB 6CNI · PDBe 6CNI · UniProt Q96HS1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.