Research workbench
Photorhabdus asymbiotica lectin (phl) in complex with synthetic C- fucoside
Analyse Photorhabdus asymbiotica lectin (phl) in complex with synthetic C- fucoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FLU
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photorhabdus asymbitoca lectin phl
- UniProt
- C7BLE4
- Ligands
- DTK, NA, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photorhabdus asymbitoca lectin phl | protein | 347 | 0% helix, 45% strand | C7BLE4 |
| B | Photorhabdus asymbitoca lectin phl | protein | 344 | 0% helix, 47% strand | C7BLE4 |
Ligands and binding sites
- DTK · (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R}, 6~{S})-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol · ligand · 12 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.81 | 0.88 | 40 | empty |
| 2 | 495 | 0.81 | 0.87 | 52 | empty |
| 3 | 131 | 0.53 | 0.81 | 36 | empty |
| 4 | 127 | 0.35 | 0.72 | 22 | empty |
| 5 | 59 | 0.35 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1104 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6FLU · Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside · 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 C7BLE4
- Elsewhere: RCSB PDB 6FLU · PDBe 6FLU · UniProt C7BLE4
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