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
- 6SLI
- Type
- protein
- Length
- 5,580 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein ragb; Raga protein; Ala-ser-thr-thr-gly-gly-asn-ser-gln-arg-gly-ser-gly…
- UniProt
- F5H948, Q7MXJ7
- Ligands
- 5PL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, I | Lipoprotein ragb | protein | 482 | 43% helix, 9% strand | F5H948 |
| B, D, G, J | Raga protein | protein | 900 | 9% helix, 43% strand | Q7MXJ7 |
| P, H | Ala-ser-thr-thr-gly-gly-asn-ser-gln-arg-gly-ser-gly | protein | 13 | 0% helix, 0% strand | — |
| E, K | Asttggnsqrggg | 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
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 2 copies · chains B
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 | 904 | 0.85 | 0.87 | 111 | empty |
| 2 | 1101 | 0.83 | 0.84 | 96 | empty |
| 3 | 1186 | 0.82 | 0.83 | 129 | empty |
| 4 | 221 | 0.82 | 0.96 | 44 | empty |
| 5 | 212 | 0.82 | 0.96 | 44 | empty |
Interfaces
17 interfaces between chains.
- C–D · 3784 Ų buried · 44 hydrogen bonds · protein-protein
- F–G · 3772 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3755 Ų buried · 33 hydrogen bonds · protein-protein
- I–J · 3734 Ų buried · 40 hydrogen bonds · protein-protein
- G–J · 2911 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6SLI · Structure of the RagAB peptide transporter · 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 6SLI · PDBe 6SLI · UniProt F5H948 · UniProt Q7MXJ7
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