MolNFT v1 · #151115 · protein
Pseudomonas aeruginosa seryl-tRNA synthetase in complex with 5'-O-(N- (L-seryl)-SULFAMOYL)URIDINE
6HDZ · Serine--tRNA ligase: “Pseudomonas aeruginosa seryl-tRNA synthetase in complex with 5'-O-(N- (L-seryl)-SULFAMOYL)URIDINE”. X-ray diffraction, 2 ligands (FZK, NA), 6 pockets (best druggability 0.82). MolNFT v1 #151115 on GenesisL1: 3D…
- PDB
- 6HDZ
- Type
- protein
- Length
- 798 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
- FZK, NA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase (EC 6.1.1.11) | protein | 421 | 46% helix, 22% strand | A0A3P3Q1W7 |
| B | Serine--tRNA ligase (EC 6.1.1.11) | protein | 377 | 40% helix, 24% strand | A0A3P3Q1W7 |
Ligands and binding sites
- FZK · 5'-O-(N-(L-seryl)-Sulfamoyl)uridine · 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 | 161 | 0.82 | 0.97 | 32 | empty |
| 2 | 627 | 0.73 | 0.81 | 63 | FZK, NA |
| 3 | 516 | 0.71 | 0.80 | 45 | EDO, FZK, NA |
| 4 | 67 | 0.37 | 0.78 | 17 | empty |
| 5 | 81 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2257 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 6HDZ · 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 6HDZ · PDBe 6HDZ · UniProt A0A3P3Q1W7
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