MolNFT v1 · #151119 · protein
Pseudomonas aeruginosa seryl-tRNA synthetase in complex with 5'-O-(N- (L-seryl)-SULFAMOYL)CYTIDINE
6HE3 · Serine--tRNA ligase: “Pseudomonas aeruginosa seryl-tRNA synthetase in complex with 5'-O-(N- (L-seryl)-SULFAMOYL)CYTIDINE”. X-ray diffraction, 2 ligands (FZQ, NA), 6 pockets (best druggability 0.82). MolNFT v1 #151119 on GenesisL1…
- PDB
- 6HE3
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase
- EC
- 6.1.1.11
- UniProt
- A0A3P3Q1W7
- Ligands
- FZQ, NA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase (EC 6.1.1.11) | protein | 422 | 45% helix, 22% strand | A0A3P3Q1W7 |
| B | Serine--tRNA ligase (EC 6.1.1.11) | protein | 377 | 38% helix, 24% strand | A0A3P3Q1W7 |
Ligands and binding sites
- FZQ · 5'-O-(N-(L-seryl)-sulfamoyl)cytidine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.82 | 0.97 | 31 | empty |
| 2 | 580 | 0.73 | 0.81 | 45 | FZQ, NA |
| 3 | 511 | 0.72 | 0.82 | 44 | EDO, FZQ, NA |
| 4 | 64 | 0.38 | 0.79 | 16 | empty |
| 5 | 73 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2241 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 6HE3 · Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with… · 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 A0A3P3Q1W7
- Elsewhere: RCSB PDB 6HE3 · PDBe 6HE3 · UniProt A0A3P3Q1W7
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