MolNFT v1 · #98833 · protein
Substrate bound outward-open state of the symporter betp
4LLH · Glycine betaine transporter betp: “Substrate bound outward-open state of the symporter betp”. X-ray diffraction, 4 ligands (1Y8, CM5, NA), 20 pockets (best druggability 0.75). MolNFT v1 #98833 on GenesisL1: 3D structure, binding…
- PDB
- 4LLH
- Type
- protein
- Length
- 1,506 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine betaine transporter betp
- UniProt
- P54582
- Ligands
- 1Y8, CM5, NA, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine betaine transporter betp | protein | 524 | 69% helix, 0% strand | P54582 |
| B | Glycine betaine transporter betp | protein | 492 | 72% helix, 0% strand | P54582 |
| C | Glycine betaine transporter betp | protein | 490 | 75% helix, 0% strand | P54582 |
Ligands and binding sites
- 1Y8 · 2-(trimethyl-lambda~5~-arsanyl)ethanol · ligand · 3 copies · chains A, B, C
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.75 | 0.80 | 87 | empty |
| 2 | 399 | 0.74 | 0.84 | 48 | 1Y8 |
| 3 | 341 | 0.67 | 0.81 | 42 | 1Y8 |
| 4 | 258 | 0.60 | 0.79 | 48 | empty |
| 5 | 179 | 0.56 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1002 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 727 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 704 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4LLH · Substrate bound outward-open state of the symporter BetP · 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 0.99
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 4LLH · PDBe 4LLH · UniProt P54582
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