MolNFT v1 · #57340 · protein
Crystal structure of archaeal O-phosphoseryl-TRNA(SEC) kinase
3A4N · L-seryl-TRNA(SEC) kinase: “Crystal structure of archaeal O-phosphoseryl-TRNA(SEC) kinase”. X-ray diffraction, 2 ligands (PO4, IOD), 5 pockets (best druggability 0.77). MolNFT v1 #57340 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3A4N
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-seryl-TRNA(SEC) kinase
- EC
- 2.7.1.-
- UniProt
- Q58933
- Ligands
- PO4, IOD
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-seryl-TRNA(SEC) kinase (EC 2.7.1.-) | protein | 237 | 59% helix, 11% strand | Q58933 |
| B | L-seryl-TRNA(SEC) kinase (EC 2.7.1.-) | protein | 237 | 58% helix, 11% strand | Q58933 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- IOD · Iodide ion · ion · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.77 | 0.83 | 65 | EDO, PO4 |
| 2 | 625 | 0.76 | 0.82 | 68 | PO4 |
| 3 | 182 | 0.56 | 0.80 | 32 | IOD |
| 4 | 190 | 0.48 | 0.76 | 27 | empty |
| 5 | 75 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 12 hydrogen bonds · protein-protein
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 Q58933
- Elsewhere: RCSB PDB 3A4N · PDBe 3A4N · UniProt Q58933
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