MolNFT v1 · #150390 · protein

Crystal structure of peptide transporter dtpa-nanobody in complex with valganciclovir

6GS4 · Dipeptide and tripeptide permease a: “Crystal structure of peptide transporter dtpa-nanobody in complex with valganciclovir”. X-ray diffraction, 1 ligand (F9E), 6 pockets (best druggability 0.79). MolNFT v1 #150390 on GenesisL1: 3D…

PDB: 6GS4
Type: protein
Length: 593 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptide and tripeptide permease a; Nanobody
UniProt: P77304
Ligands: F9E
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptide and tripeptide permease a	protein	468	81% helix, 1% strand	P77304
H	Nanobody	protein	125	5% helix, 47% strand	—

Ligands and binding sites

F9E · [(2~{S})-2-[(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)methoxy]-3-oxidanyl-propyl] (2~{S})-2-azanyl-3-methyl-butanoate · ligand · chains A
LMT · Dodecyl-beta-D-maltoside · additive · chains A

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

Pockets

6 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	976	0.79	0.80	61	F9E
2	126	0.51	0.80	21	empty
3	152	0.45	0.76	26	empty
4	72	0.39	0.78	10	empty
5	67	0.34	0.76	14	empty

Interfaces

1 interface between chains.

A–H · 896 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6GS4 · Crystal structure of peptide transporter DtpA-nanobody in complex with valganciclovir · the same entry in another collection · chain A against A, TM-score 1.00
P77304 · AlphaFold monomer V2.0 prediction for dipeptide and tripeptide permease a (P77304) · a predicted model of the same protein · chain A 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 P77304
Elsewhere: RCSB PDB 6GS4 · PDBe 6GS4 · UniProt P77304

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