Research workbench
Structure of the ragab peptide transporter
Analyse Structure of the ragab peptide transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SLJ
- Type
- protein
- Length
- 2,785 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Raga protein; Lipoprotein ragb; Ala-ser-thr-thr-gly-ala-asn-ser-gln-arg-gly-ser-gly…
- UniProt
- Q7MXJ7, F5H948
- Ligands
- 3PE, PLM
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Raga protein | protein | 900 | 11% helix, 47% strand | Q7MXJ7 |
| A | Raga protein | protein | 898 | 11% helix, 46% strand | Q7MXJ7 |
| C, D | Lipoprotein ragb | protein | 482 | 44% helix, 9% strand | F5H948 |
| P | Ala-ser-thr-thr-gly-ala-asn-ser-gln-arg-gly-ser-gly | protein | 13 | 0% helix, 0% strand | — |
| Q | Ala-ser-thr-thr-gly-ala-asn-ser-gln-arg | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains B, A, D, C
- PLM · Palmitic acid · ligand · 2 copies · chains C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains B, D, A, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 2 copies · chains B, A
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 | 1039 | 0.84 | 0.85 | 131 | empty |
| 2 | 1058 | 0.83 | 0.84 | 109 | C8E, LMT |
| 3 | 1001 | 0.82 | 0.83 | 106 | empty |
| 4 | 154 | 0.80 | 0.97 | 35 | empty |
| 5 | 164 | 0.80 | 0.96 | 35 | empty |
Interfaces
9 interfaces between chains.
- B–D · 3821 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 3817 Ų buried · 43 hydrogen bonds · protein-protein
- B–A · 2977 Ų buried · 23 hydrogen bonds · protein-protein
- B–P · 701 Ų buried · 11 hydrogen bonds · protein-protein
- A–Q · 614 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 lipid (covalent ligand, palmitoylation).
Compared structures
- 6SLJ · Structure of the RagAB peptide transporter · the same entry in another collection · chain B against B, 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 Q7MXJ7
- Every structure of UniProt F5H948
- Elsewhere: RCSB PDB 6SLJ · PDBe 6SLJ · UniProt Q7MXJ7 · UniProt F5H948
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