Research workbench
Methylated PILT4 from geobacter metallireducens bound to sulfate: C3OCOCOC conformation
Analyse Methylated PILT4 from geobacter metallireducens bound to sulfate: C3OCOCOC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OJY
- Type
- protein
- Length
- 2,123 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twitching motility pilus retraction ATPase
- UniProt
- Q39VU6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Twitching motility pilus retraction ATPase | protein | 353 | 40% helix, 26% strand | Q39VU6 |
| B | Twitching motility pilus retraction ATPase | protein | 355 | 40% helix, 26% strand | Q39VU6 |
| C | Twitching motility pilus retraction ATPase | protein | 355 | 41% helix, 26% strand | Q39VU6 |
| D | Twitching motility pilus retraction ATPase | protein | 352 | 42% helix, 26% strand | Q39VU6 |
| E | Twitching motility pilus retraction ATPase | protein | 356 | 40% helix, 26% strand | Q39VU6 |
| F | Twitching motility pilus retraction ATPase | protein | 352 | 41% helix, 26% strand | Q39VU6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.85 | 0.86 | 105 | SO4 |
| 2 | 1011 | 0.85 | 0.86 | 96 | SO4 |
| 3 | 946 | 0.84 | 0.86 | 109 | SO4 |
| 4 | 733 | 0.84 | 0.87 | 88 | SO4 |
| 5 | 1070 | 0.83 | 0.84 | 107 | SO4 |
Interfaces
6 interfaces between chains.
- D–E · 1493 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1473 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1446 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 1412 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1402 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (methylation).
Compared structures
- 6OJY · Methylated PilT4 from Geobacter metallireducens bound to sulfate: C3ocococ 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 6OJY · PDBe 6OJY · UniProt Q39VU6
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