Research workbench
Crystal structure of ABC sugar transporter subunit from rhodobacter sphaeroides 2.4.1
Analyse Crystal structure of ABC sugar transporter subunit from rhodobacter sphaeroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L49
- Type
- protein
- Length
- 1,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC sugar (ribose) transporter, periplasmic substrate- binding subunit
- UniProt
- Q3J3W0
- Ligands
- UNL
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC sugar (ribose) transporter, periplasmic substrate- binding subunit | protein | 282 | 45% helix, 21% strand | Q3J3W0 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.78 | 0.82 | 79 | UNL |
| 2 | 708 | 0.77 | 0.82 | 85 | empty |
| 3 | 75 | 0.74 | 0.97 | 18 | UNL |
| 4 | 61 | 0.72 | 0.98 | 18 | UNL |
| 5 | 372 | 0.72 | 0.83 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1000 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 997 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 413 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3L49 · CRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER SUBUNIT FROM Rhodobacter sphaeroides 2.4.1 · 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 Q3J3W0
- Elsewhere: RCSB PDB 3L49 · PDBe 3L49 · UniProt Q3J3W0
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