MolNFT v1 · #125800 · protein

Mamk double helical filament

5LJV · Actin-like ATPase: “Mamk double helical filament”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.79). MolNFT v1 #125800 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LJV
Type: protein
Length: 1,950 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-like ATPase
UniProt: Q2W8Q6
Ligands: ADP, MG
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Actin-like ATPase	protein	325	39% helix, 25% strand	Q2W8Q6

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	781	0.79	0.83	79	empty
2	737	0.79	0.83	75	empty
3	877	0.79	0.82	75	empty
4	265	0.72	0.87	40	MG, ADP
5	327	0.72	0.85	46	MG, ADP

Interfaces

7 interfaces between chains.

D–F · 968 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 966 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 964 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 963 Å² buried · 16 hydrogen bonds · protein-protein
B–E · 952 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5LJV · MamK double helical filament · the same entry in another collection · chain C against C, TM-score 1.00
Q2W8Q6 · AlphaFold monomer V2.0 prediction for actin-like protein mamk (Q2W8Q6) · a predicted model of the same protein · chain A 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 Q2W8Q6
Elsewhere: RCSB PDB 5LJV · PDBe 5LJV · UniProt Q2W8Q6

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