MolNFT v1 · #141677 · protein
Crystal structure of pilb, an extension ATPase motor of type IV pilus, from geobacter sulfurreducens
5ZFR · Type IV pilus biogenesis ATPase pilb: “Crystal structure of pilb, an extension ATPase motor of type IV pilus, from geobacter sulfurreducens”. X-ray diffraction, 2 ligands (ZN, PO4), 10 pockets (best druggability 0.82). MolNFT v1…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.