Research workbench
Crystal structure of a sugar ABC transporter (ACTODO_00688) from actinomyces odontolyticus atcc 17982 at 2.60 a resolution
Analyse Crystal structure of a sugar ABC transporter (ACTODO_00688) from actinomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BQ3
- Type
- protein
- Length
- 1,250 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnose ABC transporter, rhamnose-binding protein
- UniProt
- A7BAM4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhamnose ABC transporter, rhamnose-binding protein | protein | 313 | 42% helix, 19% strand | A7BAM4 |
| C, D | Rhamnose ABC transporter, rhamnose-binding protein | protein | 312 | 43% helix, 20% strand | A7BAM4 |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.79 | 0.83 | 78 | empty |
| 2 | 670 | 0.74 | 0.80 | 74 | empty |
| 3 | 351 | 0.59 | 0.76 | 33 | empty |
| 4 | 383 | 0.57 | 0.75 | 34 | empty |
| 5 | 244 | 0.56 | 0.78 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–C · 791 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 624 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 371 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 131 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 5BQ3 · Crystal structure of a sugar ABC transporter (ACTODO_00688) from Actinomyces… · 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 A7BAM4
- Elsewhere: RCSB PDB 5BQ3 · PDBe 5BQ3 · UniProt A7BAM4
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