MolNFT v1 · #21569 · protein + RNA
The 2.9 ångströms crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA ser
1SER · Trnaser: “The 2.9 ångströms crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA ser”. X-ray diffraction, 12 pockets (best druggability 0.80). MolNFT v1 #21569 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1SER
- Type
- protein + RNA
- Length
- 857 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trnaser; Protein (seryl-tRNA synthetase (E.C.6.1.1.11))
- UniProt
- P34945
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Trnaser | rna | 64 | — | — |
| A | Protein (seryl-tRNA synthetase (E.C.6.1.1.11)) | protein | 372 | 37% helix, 24% strand | P34945 |
| B | Protein (seryl-tRNA synthetase (E.C.6.1.1.11)) | protein | 421 | 43% helix, 21% strand | P34945 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.80 | 0.82 | 71 | empty |
| 2 | 704 | 0.76 | 0.81 | 58 | empty |
| 3 | 669 | 0.75 | 0.81 | 58 | empty |
| 4 | 84 | 0.59 | 0.87 | 22 | empty |
| 5 | 208 | 0.56 | 0.80 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2347 Ų buried · 30 hydrogen bonds · protein-protein
- T–B · 962 Ų buried · 18 hydrogen bonds · protein-nucleic
- T–A · 257 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 1SER · The 2.9 ångströms crystal structure of T. thermophilus seryl-tRNA synthetase complexed… · the same entry in another collection · chain T against T, TM-score 1.00
- P34945 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (P34945) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P34945
- Elsewhere: RCSB PDB 1SER · PDBe 1SER · UniProt P34945
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