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Crystal structure of an ABC transporter solute binding protein from thermotoga lettingae tmo (TLET_1705, target efi-510544) bound with alpha-D-tagatose
Analyse Crystal structure of an ABC transporter solute binding protein from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CI5
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein family 1
- UniProt
- A8F7X5
- Ligands
- T6T
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein family 1 | protein | 393 | 51% helix, 16% strand | A8F7X5 |
| B | Extracellular solute-binding protein family 1 | protein | 392 | 50% helix, 17% strand | A8F7X5 |
Ligands and binding sites
- T6T · alpha-D-tagatopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.78 | 0.81 | 103 | empty |
| 2 | 288 | 0.57 | 0.77 | 42 | empty |
| 3 | 126 | 0.54 | 0.82 | 19 | empty |
| 4 | 72 | 0.37 | 0.77 | 18 | empty |
| 5 | 60 | 0.32 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 5CI5 · Crystal Structure of an ABC transporter Solute Binding Protein from Thermotoga Lettingae… · the same entry in another collection · chain A against A, 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 A8F7X5
- Elsewhere: RCSB PDB 5CI5 · PDBe 5CI5 · UniProt A8F7X5
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