MolNFT v1 · #53041 · protein
Crystal structure of the sodium-coupled glycine betaine symporter betp from corynebacterium glutamicum with bound substrate
2WIT · Glycine betaine transporter betp: “Crystal structure of the sodium-coupled glycine betaine symporter betp from corynebacterium glutamicum with…”. X-ray diffraction, 1 ligand (BET), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 2WIT
- Type
- protein
- Length
- 1,541 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine betaine transporter betp
- UniProt
- P54582
- Ligands
- BET
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine betaine transporter betp | protein | 531 | 77% helix, 0% strand | P54582 |
| B | Glycine betaine transporter betp | protein | 500 | 75% helix, 0% strand | P54582 |
| C | Glycine betaine transporter betp | protein | 510 | 76% helix, 0% strand | P54582 |
Ligands and binding sites
- BET · Trimethyl glycine · ligand · 3 copies · chains A, B, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.78 | 0.87 | 49 | BET |
| 2 | 442 | 0.76 | 0.85 | 54 | BET |
| 3 | 428 | 0.76 | 0.85 | 58 | BET |
| 4 | 655 | 0.74 | 0.81 | 64 | empty |
| 5 | 318 | 0.57 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 985 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 967 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 716 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 2WIT · Crystal structure of the sodium-coupled glycine betaine symporter betp from… · 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 2WIT · PDBe 2WIT · UniProt P54582
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