Research workbench
Pilb from geobacter metallireducens bound to ADP
Analyse Pilb from geobacter metallireducens bound to ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TSG
- Type
- protein
- Length
- 1,149 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV pilus biogenesis ATPase pilb
- UniProt
- Q39VU7
- Ligands
- ADP, ZN, MG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Type IV pilus biogenesis ATPase pilb | protein | 384 | 36% helix, 27% strand | Q39VU7 |
| C | Type IV pilus biogenesis ATPase pilb | protein | 381 | 36% helix, 26% strand | Q39VU7 |
| D | Type IV pilus biogenesis ATPase pilb | protein | 384 | 34% helix, 25% strand | Q39VU7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, C
- ZN · Zinc ion · metal · 3 copies · chains B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, C
- FMT · Formic acid · additive · chains D
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 | 1188 | 0.84 | 0.85 | 111 | ADP, MG |
| 2 | 728 | 0.84 | 0.87 | 89 | ADP, MG |
| 3 | 302 | 0.68 | 0.83 | 44 | empty |
| 4 | 565 | 0.65 | 0.76 | 51 | FMT |
| 5 | 89 | 0.62 | 0.89 | 18 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1418 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1326 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5TSG · PilB from Geobacter metallireducens bound to ADP · the same entry in another collection · chain B against B, 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 Q39VU7
- Elsewhere: RCSB PDB 5TSG · PDBe 5TSG · UniProt Q39VU7
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