Research workbench
Structure of a non-canonical ABC transporter from streptococcus pneumoniae R6
Analyse Structure of a non-canonical ABC transporter from streptococcus pneumoniae R6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XU1
- Type
- protein
- Length
- 1,215 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter ATP-binding protein; ABC transporter permeae
- UniProt
- Q8DQF8, Q8DQF7
- Ligands
- MG
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter ATP-binding protein | protein | 221 | 37% helix, 28% strand | Q8DQF8 |
| B | ABC transporter ATP-binding protein | protein | 226 | 38% helix, 29% strand | Q8DQF8 |
| M | ABC transporter permeae | protein | 390 | 59% helix, 15% strand | Q8DQF7 |
| S | ABC transporter permeae | protein | 378 | 59% helix, 14% strand | Q8DQF7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.76 | 0.78 | 78 | empty |
| 2 | 487 | 0.72 | 0.81 | 59 | MG |
| 3 | 615 | 0.72 | 0.79 | 48 | empty |
| 4 | 201 | 0.61 | 0.82 | 25 | empty |
| 5 | 165 | 0.57 | 0.81 | 24 | empty |
Interfaces
4 interfaces between chains.
- M–S · 1229 Ų buried · 9 hydrogen bonds · protein-protein
- A–S · 990 Ų buried · 6 hydrogen bonds · protein-protein
- B–M · 921 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 239 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5XU1 · Structure of a non-canonical ABC transporter from Streptococcus pneumoniae R6 · 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 Q8DQF8
- Every structure of UniProt Q8DQF7
- Elsewhere: RCSB PDB 5XU1 · PDBe 5XU1 · UniProt Q8DQF8 · UniProt Q8DQF7
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