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Crystal structure of pilb, an extension ATPase motor of type IV pilus, from geobacter sulfurreducens
Analyse Crystal structure of pilb, an extension ATPase motor of type IV pilus, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZFR
- Type
- protein
- Length
- 1,154 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV pilus biogenesis ATPase pilb
- UniProt
- Q74D28
- Ligands
- ZN, PO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV pilus biogenesis ATPase pilb | protein | 383 | 37% helix, 27% strand | Q74D28 |
| B | Type IV pilus biogenesis ATPase pilb | protein | 385 | 38% helix, 26% strand | Q74D28 |
| C | Type IV pilus biogenesis ATPase pilb | protein | 386 | 37% helix, 27% strand | Q74D28 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.82 | 0.84 | 74 | PO4 |
| 2 | 639 | 0.74 | 0.81 | 76 | PO4 |
| 3 | 846 | 0.70 | 0.76 | 55 | PO4 |
| 4 | 365 | 0.59 | 0.77 | 45 | empty |
| 5 | 153 | 0.56 | 0.82 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1748 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1626 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5ZFR · Crystal structure of PilB, an extension ATPase motor of Type IV pilus, from Geobacter… · 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 Q74D28
- Elsewhere: RCSB PDB 5ZFR · PDBe 5ZFR · UniProt Q74D28
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