Research workbench

Crystal structure of E.COLI MULTIDRUG/H+ antiporter mdfa in outward open conformation with bound Fab fragment

Analyse Crystal structure of E.COLI MULTIDRUG/H+ antiporter mdfa in outward open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GV1
Type: protein
Length: 806 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major facilitator superfamily MULTIDRUG/H+ antiporter mdfa from E.COLI; Fab fragment…
UniProt: P0AEY8
Ligands: SO4
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major facilitator superfamily MULTIDRUG/H+ antiporter mdfa from E.COLI	protein	387	85% helix, 0% strand	P0AEY8
H	Fab fragment YN1074 heavy chain	protein	208	3% helix, 51% strand	—
L	Fab fragment YN1074 light chain	protein	211	5% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1076	0.82	0.82	50	empty
2	347	0.65	0.80	38	empty
3	297	0.51	0.74	47	empty
4	87	0.47	0.81	23	empty
5	73	0.32	0.75	16	empty

Interfaces

3 interfaces between chains.

H–L · 1747 Å² buried · 19 hydrogen bonds · protein-protein
A–H · 629 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 390 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6GV1 · Crystal structure of E.coli Multidrug/H+ antiporter MdfA in outward open conformation… · the same entry in another collection · chain A against A, TM-score 1.00
P0AEY8 · AlphaFold monomer V2.0 prediction for multidrug transporter mdfa (P0AEY8) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 P0AEY8
Elsewhere: RCSB PDB 6GV1 · PDBe 6GV1 · UniProt P0AEY8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.