Research workbench
Structure of the ragab peptide importer in the 'closed-closed' state
Analyse Structure of the ragab peptide importer in the 'closed-closed' state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SM3
- Type
- protein
- Length
- 1,398 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein ragb; Raga protein; Gly-gly-ala-thr-thr-ala-thr-thr-thr-thr-ser-thr-ser
- UniProt
- F5H948, Q7MXJ7
- Ligands
- 5PL, PLM
- Pockets
- 17 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein ragb | protein | 482 | 38% helix, 9% strand | F5H948 |
| B | Raga protein | protein | 903 | 7% helix, 46% strand | Q7MXJ7 |
| C | Gly-gly-ala-thr-thr-ala-thr-thr-thr-thr-ser-thr-ser | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- 5PL · (1R,4S,6R)-6-({[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}methyl)-4-hydroxy-1-{[(15-methylhexadecanoyl)oxy]methyl}-4-oxido-7-oxo-3,5-dioxa-8-aza-4-phosphaheptacos-1-yl 15-methylhexadecanoate · ligand · chains A, B
- PLM · Palmitic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.81 | 0.82 | 133 | empty |
| 2 | 184 | 0.81 | 0.96 | 35 | empty |
| 3 | 719 | 0.74 | 0.80 | 103 | empty |
| 4 | 728 | 0.73 | 0.79 | 87 | empty |
| 5 | 160 | 0.72 | 0.90 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3822 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 754 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, palmitoylation).
Compared structures
- 6SM3 · Structure of the RagAB peptide importer in the 'closed-closed' state · 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 F5H948
- Every structure of UniProt Q7MXJ7
- Elsewhere: RCSB PDB 6SM3 · PDBe 6SM3 · UniProt F5H948 · UniProt Q7MXJ7
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