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Structure of a bacterial ATM1-family ABC transporter

Analyse Structure of a bacterial ATM1-family ABC transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MRV
Type: protein
Length: 1,198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter related protein
UniProt: Q2G506
Ligands: HGD, PO4
Pockets: 17 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC transporter related protein	protein	600	65% helix, 10% strand	Q2G506
B	ABC transporter related protein	protein	598	65% helix, 10% strand	Q2G506

Ligands and binding sites

HGD · mercury bis(L-gamma-glutamyl-3-sulfido-L-alanylglycine) · ligand · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B
LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.86	0.87	102	empty
2	471	0.77	0.84	43	LDA
3	360	0.77	0.86	41	LDA
4	175	0.67	0.87	26	empty
5	377	0.62	0.78	54	empty

Interfaces

1 interface between chains.

A–B · 6320 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

4MRV · Structure of a bacterial Atm1-family ABC transporter · the same entry in another collection · chain A against A, TM-score 1.00
Q2G506 · AlphaFold monomer V2.0 prediction for ATM1-type heavy metal exporter (Q2G506) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q2G506
Elsewhere: RCSB PDB 4MRV · PDBe 4MRV · UniProt Q2G506

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