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Structure of ATATM3 in the closed conformation

Analyse Structure of ATATM3 in the closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N5A
Type: protein
Length: 1,178 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter B family member 25, mitochondrial
UniProt: Q9LVM1
Ligands: ADP, MG, VO4
Pockets: 18 · best druggability 0.89

Structure

electron microscopy · 1 distinct chain · 60% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ABC transporter B family member 25, mitochondrial	protein	589	60% helix, 9% strand	Q9LVM1

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
VO4 · Vanadate ion · ion · 2 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	822	0.89	0.92	96	empty
2	919	0.89	0.91	121	ADP, VO4, MG
3	262	0.82	0.94	46	empty
4	256	0.81	0.93	49	empty
5	103	0.75	0.95	23	empty

Interfaces

1 interface between chains.

A–B · 7330 Å² buried · 65 hydrogen bonds · protein-protein

Compared structures

7N5A · Structure of AtAtm3 in the closed conformation · the same entry in another collection · chain A against A, TM-score 1.00
Q9LVM1 · AlphaFold monomer V2.0 prediction for ABC transporter B family member 25, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.87

Analyse

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Every structure of UniProt Q9LVM1
Elsewhere: RCSB PDB 7N5A · PDBe 7N5A · UniProt Q9LVM1

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