Research workbench
Structure of knotted yibk from P. aeruginosa
Analyse Structure of knotted yibk from P. aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QH8
- Type
- protein
- Length
- 627 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (CYTIDINE(34)-2'-O)-methyltransferase
- EC
- 2.1.1.207
- UniProt
- A0A071LCY6
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 162 | 36% helix, 17% strand | A0A071LCY6 |
| B | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 153 | 30% helix, 18% strand | A0A071LCY6 |
| C | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 157 | 30% helix, 17% strand | A0A071LCY6 |
| D | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 155 | 28% helix, 17% strand | A0A071LCY6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.77 | 0.82 | 68 | SO4 |
| 2 | 485 | 0.71 | 0.81 | 49 | SO4 |
| 3 | 176 | 0.65 | 0.85 | 25 | SO4 |
| 4 | 149 | 0.61 | 0.84 | 22 | SO4 |
| 5 | 196 | 0.50 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1572 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1363 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 384 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6QH8 · Structure of knotted YibK from P. aeruginosa · 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 A0A071LCY6
- Elsewhere: RCSB PDB 6QH8 · PDBe 6QH8 · UniProt A0A071LCY6
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