MolNFT v1 · #74551 · protein

Crystal structure of betp-G153D with choline bound

3P03 · Glycine betaine transporter betp: “Crystal structure of betp-G153D with choline bound”. X-ray diffraction, 1 ligand (CHT), 20 pockets (best druggability 0.81). MolNFT v1 #74551 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3P03
Type: protein
Length: 1,488 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine betaine transporter betp
UniProt: P54582
Ligands: CHT
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycine betaine transporter betp	protein	504	70% helix, 0% strand	P54582
B	Glycine betaine transporter betp	protein	476	67% helix, 0% strand	P54582
C	Glycine betaine transporter betp	protein	508	76% helix, 0% strand	P54582

Ligands and binding sites

CHT · Choline ion · ligand · chains C

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

Pockets

20 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	437	0.81	0.88	70	empty
2	542	0.75	0.82	49	CHT
3	82	0.74	0.97	21	empty
4	1174	0.74	0.77	112	empty
5	297	0.67	0.82	44	empty

Interfaces

3 interfaces between chains.

A–C · 1056 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 928 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 737 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3P03 · Crystal structure of BetP-G153D with choline bound · the same entry in another collection · chain A against A, TM-score 1.00
P54582 · AlphaFold monomer V2.0 prediction for glycine betaine transporter betp (P54582) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P54582
Elsewhere: RCSB PDB 3P03 · PDBe 3P03 · UniProt P54582

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