Research workbench
Klebsiella pneumoniae seryl-tRNA synthetase in complex with compound SERS7HMDDA
Analyse Klebsiella pneumoniae seryl-tRNA synthetase in complex with compound SERS7HMDDA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AP1
- Type
- protein
- Length
- 421 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
- W9BNU9
- Ligands
- RUZ, CA
- Pockets
- 3 · best druggability 0.75
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 | 421 | 45% helix, 21% strand | W9BNU9 |
Ligands and binding sites
- RUZ · [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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 | 587 | 0.75 | 0.82 | 52 | RUZ, EDO, CA |
| 2 | 158 | 0.55 | 0.80 | 20 | empty |
| 3 | 94 | 0.39 | 0.76 | 17 | empty |
Compared structures
- 7AP1 · Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA · 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 W9BNU9
- Elsewhere: RCSB PDB 7AP1 · PDBe 7AP1 · UniProt W9BNU9
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