MolNFT v1 · #157854 · protein
Crystal structure of tryptophan-tRNA ligase from chlamydia trachomatis with bound L-tryptophan
6NCR · Tryptophan--tRNA ligase: “Crystal structure of tryptophan-tRNA ligase from chlamydia trachomatis with bound L-tryptophan”. X-ray diffraction, 2 ligands (TRP, CA), 7 pockets (best druggability 0.68). MolNFT v1 #157854 on GenesisL1…
- PDB
- 6NCR
- Type
- protein
- Length
- 683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan--tRNA ligase
- EC
- 6.1.1.2
- UniProt
- O84589
- Ligands
- TRP, CA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 342 | 59% helix, 9% strand | O84589 |
| B | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 341 | 58% helix, 9% strand | O84589 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.68 | 0.80 | 49 | TRP, EDO |
| 2 | 417 | 0.65 | 0.78 | 47 | TRP, EDO |
| 3 | 58 | 0.49 | 0.86 | 17 | ACT |
| 4 | 174 | 0.49 | 0.77 | 35 | empty |
| 5 | 75 | 0.40 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2686 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6NCR · Crystal Structure of Tryptophan-tRNA ligase from Chlamydia trachomatis with bound… · the same entry in another collection · chain A against A, TM-score 1.00
- O84589 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (O84589) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O84589
- Elsewhere: RCSB PDB 6NCR · PDBe 6NCR · UniProt O84589
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