Research workbench
Structure of the ragab peptide importer in the 'open-closed' state
Analyse Structure of the ragab peptide importer in the 'open-closed' state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SMQ
- Type
- protein
- Length
- 2,791 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein ragb; Raga protein; Ser-gly-ala-thr-thr-ala-thr-thr-thr-thr-ser-asn-ser
- UniProt
- F5H948, Q7MXJ7
- Ligands
- 5PL, PLM
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lipoprotein ragb | protein | 482 | 38% helix, 9% strand | F5H948 |
| B | Raga protein | protein | 903 | 9% helix, 47% strand | Q7MXJ7 |
| C | Ser-gly-ala-thr-thr-ala-thr-thr-thr-thr-ser-asn-ser | protein | 13 | 0% helix, 0% strand | — |
| E | Raga protein | protein | 911 | 8% helix, 44% strand | Q7MXJ7 |
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 · 2 copies · chains A, B, D, E
- PLM · Palmitic acid · ligand · 2 copies · chains A, D
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 5 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.82 | 0.83 | 85 | C8E |
| 2 | 1184 | 0.81 | 0.82 | 146 | empty |
| 3 | 183 | 0.81 | 0.96 | 38 | empty |
| 4 | 179 | 0.80 | 0.96 | 37 | empty |
| 5 | 831 | 0.76 | 0.80 | 92 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3842 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2819 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2155 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 773 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 lipid (covalent ligand, palmitoylation).
Compared structures
- 6SMQ · Structure of the RagAB peptide importer in the 'open-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 6SMQ · PDBe 6SMQ · UniProt F5H948 · UniProt Q7MXJ7
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