Research workbench
Bacterial dynamin-like protein lipid tube bound
Analyse Bacterial dynamin-like protein lipid tube bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W6D
- Type
- protein
- Length
- 1,360 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin family protein
- UniProt
- B2IZD3
- Ligands
- CPL, GDP
- Pockets
- 16 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 66% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dynamin family protein | protein | 680 | 66% helix, 8% strand | B2IZD3 |
Ligands and binding sites
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 44 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.84 | 0.90 | 67 | GDP |
| 2 | 500 | 0.83 | 0.90 | 63 | GDP |
| 3 | 87 | 0.75 | 0.97 | 22 | empty |
| 4 | 430 | 0.75 | 0.84 | 53 | empty |
| 5 | 52 | 0.67 | 0.96 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3146 Ų buried · 151 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
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 B2IZD3
- Elsewhere: RCSB PDB 2W6D · PDBe 2W6D · UniProt B2IZD3
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