MolNFT v1 · #164047 · protein
Structure of the ragab peptide transporter
6SLN · Raga protein: “Structure of the ragab peptide transporter”. X-ray diffraction, 2 ligands (3PE, PLM), 20 pockets (best druggability 0.83). MolNFT v1 #164047 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SLN
- Type
- protein
- Length
- 2,794 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Raga protein; Lipoprotein ragb; Gln-thr-ala-gly-ala-asn-ser-gln-arg-gly-ser-ala-gly
- UniProt
- Q7MXJ7, F5H948
- Ligands
- 3PE, PLM
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Raga protein | protein | 903 | 12% helix, 49% strand | Q7MXJ7 |
| B | Raga protein | protein | 902 | 11% helix, 49% strand | Q7MXJ7 |
| C | Lipoprotein ragb | protein | 481 | 46% helix, 10% strand | F5H948 |
| D | Lipoprotein ragb | protein | 482 | 44% helix, 11% strand | F5H948 |
| P, Q | Gln-thr-ala-gly-ala-asn-ser-gln-arg-gly-ser-ala-gly | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, D, B, C
- PLM · Palmitic acid · ligand · 2 copies · chains C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 4 copies · chains A, B, D, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 3 copies · chains A, 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 | 954 | 0.83 | 0.84 | 103 | empty |
| 2 | 1053 | 0.82 | 0.83 | 118 | empty |
| 3 | 883 | 0.81 | 0.83 | 79 | C8E |
| 4 | 144 | 0.80 | 0.97 | 34 | empty |
| 5 | 135 | 0.79 | 0.96 | 35 | empty |
Interfaces
9 interfaces between chains.
- B–C · 3735 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 3692 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3023 Ų buried · 31 hydrogen bonds · protein-protein
- A–Q · 755 Ų buried · 11 hydrogen bonds · protein-protein
- B–P · 718 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 lipid (covalent ligand, palmitoylation).
Compared structures
- 6SLN · 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 Q7MXJ7
- Every structure of UniProt F5H948
- Elsewhere: RCSB PDB 6SLN · PDBe 6SLN · UniProt Q7MXJ7 · UniProt F5H948
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