Research workbench
Pilb from geobacter metallireducens bound to AMP-pnp
Analyse Pilb from geobacter metallireducens bound to AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TSH
- Type
- protein
- Length
- 2,281 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV pilus biogenesis ATPase pilb
- UniProt
- Q39VU7
- Ligands
- ANP, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV pilus biogenesis ATPase pilb | protein | 375 | 39% helix, 27% strand | Q39VU7 |
| B | Type IV pilus biogenesis ATPase pilb | protein | 376 | 39% helix, 26% strand | Q39VU7 |
| C | Type IV pilus biogenesis ATPase pilb | protein | 382 | 38% helix, 28% strand | Q39VU7 |
| D | Type IV pilus biogenesis ATPase pilb | protein | 379 | 38% helix, 27% strand | Q39VU7 |
| E | Type IV pilus biogenesis ATPase pilb | protein | 387 | 37% helix, 27% strand | Q39VU7 |
| F | Type IV pilus biogenesis ATPase pilb | protein | 382 | 38% helix, 27% strand | Q39VU7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.85 | 0.86 | 106 | ADP |
| 2 | 1199 | 0.83 | 0.84 | 101 | ADP |
| 3 | 841 | 0.82 | 0.85 | 96 | ANP, MG |
| 4 | 1035 | 0.80 | 0.81 | 89 | ANP, MG |
| 5 | 397 | 0.71 | 0.83 | 48 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1671 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 1654 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 1588 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1534 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1496 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5TSH · PilB from Geobacter metallireducens bound to AMP-PNP · 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 Q39VU7
- Elsewhere: RCSB PDB 5TSH · PDBe 5TSH · UniProt Q39VU7
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