Research workbench
Whole structure of a 15-stranded parm filament from clostridium botulinum
Analyse Whole structure of a 15-stranded parm filament from clostridium botulinum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IZR
- Type
- protein
- Length
- 10,470 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative plasmid segregation protein parm
- UniProt
- A0A0B4W229
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, A, B, D, E, G, H, J, K, M, N, P, Q, b, c, e, f, h, i, k, l, n, o, q, r, t, u, w, x | Putative plasmid segregation protein parm | protein | 349 | 31% helix, 24% strand | A0A0B4W229 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 30 copies · chains 1, 2, A, B, D, E, G, H, J, K, M, N, P, Q, b, c, e, f, h, i, k, l, n, o, q, r, t, u, w, x
- MG · Magnesium ion · metal · 30 copies · chains 1, 2, A, B, D, E, G, H, J, K, M, N, P, Q, b, c, e, f, h, i, k, l, n, o, q, r, t, u, w, x
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 | 699 | 0.76 | 0.81 | 83 | ADP, MG |
| 2 | 616 | 0.75 | 0.82 | 85 | ADP, MG |
| 3 | 1096 | 0.75 | 0.77 | 88 | ADP, MG |
| 4 | 460 | 0.75 | 0.84 | 68 | ADP, MG |
| 5 | 599 | 0.75 | 0.82 | 79 | ADP, MG |
Interfaces
50 interfaces between chains.
- k–l · 1401 Ų buried · 25 hydrogen bonds · protein-protein
- 1–2 · 1349 Ų buried · 18 hydrogen bonds · protein-protein
- n–o · 1327 Ų buried · 17 hydrogen bonds · protein-protein
- q–r · 1277 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1261 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6IZR · Whole structure of a 15-stranded ParM filament from Clostridium botulinum · the same entry in another collection · chain K against K, 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 A0A0B4W229
- Elsewhere: RCSB PDB 6IZR · PDBe 6IZR · UniProt A0A0B4W229
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