MolNFT v1 · #116944 · protein
Crystal structure of an ABC transporter periplasmic solute binding protein (IPR025997) from actinobacillus succinogenes 130Z(ASUC_0081, target efi-511065) with bound D-allose
5DTE · Monosaccharide-transporting ATPase: “Crystal structure of an ABC transporter periplasmic solute binding protein (IPR025997) from actinobacillus…”. X-ray diffraction, 1 ligand (ALL), 9 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5DTE
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monosaccharide-transporting ATPase
- EC
- 3.6.3.17
- UniProt
- A6VKG5
- Ligands
- ALL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Monosaccharide-transporting ATPase (EC 3.6.3.17) | protein | 286 | 44% helix, 20% strand | A6VKG5 |
| B | Monosaccharide-transporting ATPase (EC 3.6.3.17) | protein | 287 | 44% helix, 21% strand | A6VKG5 |
| D | Monosaccharide-transporting ATPase (EC 3.6.3.17) | protein | 281 | 47% helix, 21% strand | A6VKG5 |
Ligands and binding sites
- ALL · beta-D-allopyranose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.80 | 0.81 | 111 | empty |
| 2 | 760 | 0.79 | 0.83 | 86 | ALL |
| 3 | 153 | 0.64 | 0.86 | 29 | ALL |
| 4 | 169 | 0.52 | 0.79 | 25 | empty |
| 5 | 58 | 0.37 | 0.79 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1118 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 941 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 180 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 172 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DTE · Crystal Structure of an ABC transporter periplasmic solute binding protein (IPR025997)… · 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 A6VKG5
- Elsewhere: RCSB PDB 5DTE · PDBe 5DTE · UniProt A6VKG5
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