Research workbench

Actin-like parm protein bound to amppnp

Analyse Actin-like parm protein bound to amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AEY
Type: protein
Length: 1,590 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasmid segregation protein parm
UniProt: P11904
Ligands: ANP
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Plasmid segregation protein parm	protein	318	36% helix, 25% strand	P11904

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.76	0.88	53	ANP
2	331	0.75	0.87	59	ANP
3	360	0.74	0.85	55	ANP
4	363	0.74	0.85	59	ANP
5	352	0.74	0.86	55	ANP

Interfaces

7 interfaces between chains.

A–C · 1135 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 1132 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1128 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 434 Å² buried · 1 hydrogen bond · protein-protein
C–D · 434 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5AEY · actin-like ParM protein bound to AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
P11904 · AlphaFold monomer V2.0 prediction for plasmid segregation protein parm (P11904) · 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 P11904
Elsewhere: RCSB PDB 5AEY · PDBe 5AEY · UniProt P11904

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