Research workbench
High-resolution structure of the periplasmic ectoine- binding protein from teaabc trap-transporter of halomonas elongata
Analyse High-resolution structure of the periplasmic ectoine- binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VPN
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic substrate binding protein
- UniProt
- Q8VPB3
- Ligands
- 4CS, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic substrate binding protein | protein | 306 | 55% helix, 20% strand | Q8VPB3 |
| B | Periplasmic substrate binding protein | protein | 310 | 54% helix, 19% strand | Q8VPB3 |
Ligands and binding sites
- 4CS · (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.65 | 0.77 | 71 | 4CS |
| 2 | 144 | 0.58 | 0.83 | 33 | 4CS |
| 3 | 54 | 0.41 | 0.82 | 16 | empty |
| 4 | 78 | 0.41 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 371 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VPN · High-resolution structure of the periplasmic ectoine-binding protein from TeaABC… · the same entry in another collection · chain B against B, 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 Q8VPB3
- Elsewhere: RCSB PDB 2VPN · PDBe 2VPN · UniProt Q8VPB3
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