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Cryo-EM structure of the mpa hexamer in the presence of ATP and the pup-fabd substrate

Analyse Cryo-EM structure of the mpa hexamer in the presence of ATP and the pup-fabd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LJF
Type: protein
Length: 2,007 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aaa ATPase forming ring-shaped complexes
UniProt: A0A045JPX7
Ligands: ADP, ATP, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 4 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aaa ATPase forming ring-shaped complexes	protein	454	36% helix, 19% strand	A0A045JPX7
C	Aaa ATPase forming ring-shaped complexes	protein	427	35% helix, 24% strand	A0A045JPX7
D, E	Aaa ATPase forming ring-shaped complexes	protein	123	0% helix, 45% strand	A0A045JPX7
F	Aaa ATPase forming ring-shaped complexes	protein	426	36% helix, 23% strand	A0A045JPX7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, C
ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	181	0.81	0.95	43	empty
2	852	0.75	0.79	84	MG, ATP
3	542	0.75	0.82	67	empty
4	584	0.73	0.80	55	empty
5	674	0.72	0.79	63	empty

Interfaces

6 interfaces between chains.

A–B · 1682 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1620 Å² buried · 18 hydrogen bonds · protein-protein
A–F · 1560 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1092 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 900 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7LJF · Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A045JPX7
Elsewhere: RCSB PDB 7LJF · PDBe 7LJF · UniProt A0A045JPX7

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