Research workbench
Pglk flippase in complex with inhibitory nanobody
Analyse Pglk flippase in complex with inhibitory nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NBD
- Type
- protein
- Length
- 1,251 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlab protein; Nanobody
- UniProt
- O86150
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wlab protein | protein | 564 | 60% helix, 5% strand | O86150 |
| C | Nanobody | protein | 123 | 2% helix, 27% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.80 | 0.82 | 78 | empty |
| 2 | 233 | 0.74 | 0.89 | 32 | empty |
| 3 | 372 | 0.63 | 0.78 | 42 | empty |
| 4 | 181 | 0.58 | 0.80 | 23 | empty |
| 5 | 218 | 0.56 | 0.79 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6340 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 820 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 290 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NBD · PglK flippase in complex with inhibitory nanobody · 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 5NBD · PDBe 5NBD · UniProt O86150
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