Research workbench
PILT4 from geobacter metallireducens bound to AMP-pnp: C2CCOCCO conformation
Analyse PILT4 from geobacter metallireducens bound to AMP-pnp: C2CCOCCO conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OKV
- Type
- protein
- Length
- 2,117 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twitching motility pilus retraction ATPase
- UniProt
- Q39VU6
- Ligands
- ANP, ADP, MG
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Twitching motility pilus retraction ATPase | protein | 352 | 41% helix, 26% strand | Q39VU6 |
| B | Twitching motility pilus retraction ATPase | protein | 351 | 41% helix, 26% strand | Q39VU6 |
| C | Twitching motility pilus retraction ATPase | protein | 351 | 42% helix, 26% strand | Q39VU6 |
| D | Twitching motility pilus retraction ATPase | protein | 358 | 39% helix, 25% strand | Q39VU6 |
| E | Twitching motility pilus retraction ATPase | protein | 353 | 40% helix, 26% strand | Q39VU6 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.84 | 0.85 | 117 | ADP |
| 2 | 1039 | 0.84 | 0.85 | 105 | MG, ANP |
| 3 | 1075 | 0.84 | 0.85 | 96 | MG, ANP |
| 4 | 961 | 0.84 | 0.85 | 107 | MG, ANP |
| 5 | 1078 | 0.82 | 0.83 | 124 | ADP |
Interfaces
6 interfaces between chains.
- A–B · 1636 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 1601 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 1516 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1499 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1477 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6OKV · PilT4 from Geobacter metallireducens bound to AMP-PNP: C2ccocco conformation · 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 Q39VU6
- Elsewhere: RCSB PDB 6OKV · PDBe 6OKV · UniProt Q39VU6
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