Research workbench
High resolution structure of the periplasmic binding protein teaa from teaabc trap transporter of halomonas elongata in complex with hydroxyectoine
Analyse High resolution structure of the periplasmic binding protein teaa from teaabc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VPO
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic substrate binding protein
- UniProt
- Q8VPB3
- Ligands
- 6CS, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic substrate binding protein | protein | 307 | 53% helix, 20% strand | Q8VPB3 |
| B | Periplasmic substrate binding protein | protein | 311 | 53% helix, 19% strand | Q8VPB3 |
Ligands and binding sites
- 6CS · (4S,5S)-5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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 | 469 | 0.65 | 0.77 | 65 | 6CS |
| 2 | 167 | 0.56 | 0.81 | 31 | 6CS |
| 3 | 67 | 0.32 | 0.75 | 14 | empty |
| 4 | 96 | 0.32 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 355 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VPO · High resolution structure of the periplasmic binding protein TeaA from TeaABC TRAP… · 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 2VPO · PDBe 2VPO · UniProt Q8VPB3
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