MolNFT v1 · #129877 · protein
An oligomerised bacterial dynamin pair provides a mechanism for the long range sensing and tethering of membranes
5OXF · GTP-binding protein: “An oligomerised bacterial dynamin pair provides a mechanism for the long range sensing and tethering of…”. X-ray diffraction, 1 ligand (GDP), 20 pockets (best druggability 0.85). MolNFT v1 #129877 on GenesisL1…
- PDB
- 5OXF
- Type
- protein
- Length
- 2,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein
- UniProt
- A0A1D9BJX7, A0A1D9BKH6
- Ligands
- GDP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein | protein | 703 | 65% helix, 7% strand | A0A1D9BJX7 |
| B | GTP-binding protein | protein | 591 | 59% helix, 8% strand | A0A1D9BJX7 |
| C, D | GTP-binding protein | protein | 601 | 61% helix, 10% strand | A0A1D9BKH6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.85 | 0.87 | 81 | empty |
| 2 | 628 | 0.76 | 0.82 | 68 | GDP |
| 3 | 893 | 0.75 | 0.78 | 67 | empty |
| 4 | 628 | 0.74 | 0.81 | 60 | GDP |
| 5 | 806 | 0.73 | 0.78 | 68 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2738 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1314 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1298 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 517 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5OXF · An oligomerised bacterial dynamin pair provides a mechanism for the long range sensing… · 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 A0A1D9BJX7
- Every structure of UniProt A0A1D9BKH6
- Elsewhere: RCSB PDB 5OXF · PDBe 5OXF · UniProt A0A1D9BJX7 · UniProt A0A1D9BKH6
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