Research workbench
PilT4 from Geobacter metallireducens bound to ADP with partial occupancy: C3ocococ conformation
Analyse PilT4 from Geobacter metallireducens bound to ADP with partial occupancy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OJZ
- Type
- protein
- Length
- 2,127 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.027
- Source
- Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)
- Molecule
- Twitching motility pilus retraction ATPase
- UniProt
- Q39VU6
- Ligands
- ADP
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · resolution 3.027 · 4 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Twitching motility pilus retraction ATPase | protein | 355 | 41% helix, 26% strand | Q39VU6 |
| B, E, F | Twitching motility pilus retraction ATPase | protein | 353 | 40% helix, 26% strand | Q39VU6 |
| C | Twitching motility pilus retraction ATPase | protein | 352 | 40% helix, 26% strand | Q39VU6 |
| D | Twitching motility pilus retraction ATPase | protein | 361 | 41% helix, 25% strand | Q39VU6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.85 | 0.86 | 120 | ADP |
| 2 | 1190 | 0.82 | 0.83 | 107 | ADP |
| 3 | 934 | 0.81 | 0.83 | 75 | ADP |
| 4 | 1084 | 0.81 | 0.82 | 108 | empty |
| 5 | 944 | 0.81 | 0.83 | 73 | ADP |
Interfaces
6 interfaces between chains.
- E–F · 1691 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1659 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 1611 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1579 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 1512 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6OJZ · PILT4 from geobacter metallireducens bound to ADP with partial occupancy: C3OCOCOC… · 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 6OJZ · PDBe 6OJZ · UniProt Q39VU6
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