MolNFT v1 · #115020 · protein
ATP-driven lipid-linked oligosaccharide flippase pglk in apo-inward state (1)
5C78 · ATP-driven flippase pglk: “ATP-driven lipid-linked oligosaccharide flippase pglk in apo-inward state (1)”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #115020 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5C78
- Type
- protein
- Length
- 2,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-driven flippase pglk
- UniProt
- O86150
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ATP-driven flippase pglk | protein | 564 | 62% helix, 6% strand | O86150 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.82 | 0.83 | 83 | empty |
| 2 | 1179 | 0.81 | 0.82 | 65 | empty |
| 3 | 229 | 0.57 | 0.79 | 36 | 1PE |
| 4 | 230 | 0.54 | 0.77 | 34 | empty |
| 5 | 72 | 0.54 | 0.86 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–C · 6312 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 6223 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C78 · ATP-driven lipid-linked oligosaccharide flippase PglK in apo-inward state (1) · 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 O86150
- Elsewhere: RCSB PDB 5C78 · PDBe 5C78 · UniProt O86150
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