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Structure of a ligand free pot family peptide transporter

Analyse Structure of a ligand free pot family peptide transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D2B
Type: protein
Length: 445 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Di-or TRIPEPTIDE\:H+ symporter
UniProt: Q5M4H8
Ligands: 78N, 78M, PO4
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 82% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Di-or TRIPEPTIDE\:H+ symporter	protein	445	82% helix, 1% strand	Q5M4H8

Ligands and binding sites

78N · (2R)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 5 copies · chains A
78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 4 copies · chains A
PO4 · Phosphate ion · ion · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	833	0.78	0.81	54	empty
2	388	0.63	0.77	36	empty
3	60	0.30	0.75	15	empty

Compared structures

4D2B · Structure of a ligand free POT family peptide transporter · 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 Q5M4H8
Elsewhere: RCSB PDB 4D2B · PDBe 4D2B · UniProt Q5M4H8

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