MolNFT v1 · #151249 · protein
Klebsiella pneumoniae seryl-tRNA synthetase in complex with 5'-O-(N- (L-seryl)-SULFAMOYL)CYTIDINE
6HHZ · Serine--tRNA ligase: “Klebsiella pneumoniae seryl-tRNA synthetase in complex with 5'-O-(N- (L-seryl)-SULFAMOYL)CYTIDINE”. X-ray diffraction, 3 ligands (FZQ, CA, CL), 3 pockets (best druggability 0.74). MolNFT v1 #151249 on…
- PDB
- 6HHZ
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase
- EC
- 6.1.1.11
- UniProt
- A6T6Z0
- Ligands
- FZQ, CA, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase (EC 6.1.1.11) | protein | 428 | 45% helix, 21% strand | A6T6Z0 |
Ligands and binding sites
- FZQ · 5'-O-(N-(L-seryl)-sulfamoyl)cytidine · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.74 | 0.81 | 53 | EDO, FZQ, CA |
| 2 | 180 | 0.58 | 0.81 | 20 | 1PE |
| 3 | 86 | 0.38 | 0.77 | 17 | empty |
Compared structures
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 A6T6Z0
- Elsewhere: RCSB PDB 6HHZ · PDBe 6HHZ · UniProt A6T6Z0
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