MolNFT v2 · #116968 · protein
Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET EFI-511225) bound with alpha-D-Tagatopyranose
5DKV · ABC transporter substrate binding protein (Ribose): “Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET…”. X-ray diffraction at 1.68, 1 ligand (T6T), 7 pockets (best…
- PDB
- 5DKV
- Type
- protein
- Length
- 1,199 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.68
- Source
- Agrobacterium vitis (strain S4 / ATCC BAA-846)
- Molecule
- ABC transporter substrate binding protein (Ribose)
- UniProt
- B9K0T2
- Ligands
- T6T
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.68 · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter substrate binding protein (Ribose) | protein | 303 | 41% helix, 18% strand | B9K0T2 |
| B | ABC transporter substrate binding protein (Ribose) | protein | 300 | 42% helix, 18% strand | B9K0T2 |
| C, D | ABC transporter substrate binding protein (Ribose) | protein | 298 | 41% helix, 19% strand | B9K0T2 |
Ligands and binding sites
- T6T · alpha-D-tagatopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.78 | 0.80 | 107 | empty |
| 2 | 52 | 0.71 | 0.98 | 16 | T6T |
| 3 | 760 | 0.66 | 0.74 | 57 | empty |
| 4 | 135 | 0.45 | 0.77 | 21 | empty |
| 5 | 89 | 0.43 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 898 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 465 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 119 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DKV · Crystal structure of an ABC transporter solute binding protein from agrobacterium… · 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 B9K0T2
- Elsewhere: RCSB PDB 5DKV · PDBe 5DKV · UniProt B9K0T2
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