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Crystal structure analysis of B. stearothermophilus tryptophanyl-tRNA synthetase complexed with tryptophan, AMP, and inorganic phosphate
Analyse Crystal structure analysis of B. stearothermophilus tryptophanyl-tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FI0
- Type
- protein
- Length
- 5,367 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- TRP, AMP, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 10 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 297 | 58% helix, 8% strand | P00953 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 295 | 56% helix, 8% strand | P00953 |
| D, H, J, L, M, N, O, Q | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 301 | 57% helix, 8% strand | P00953 |
| E | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 293 | 57% helix, 8% strand | P00953 |
| F | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 296 | 58% helix, 8% strand | P00953 |
| G | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 302 | 57% helix, 9% strand | P00953 |
| I | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 298 | 56% helix, 8% strand | P00953 |
| K | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 296 | 52% helix, 8% strand | P00953 |
| P | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 295 | 55% helix, 7% strand | P00953 |
| R | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 290 | 56% helix, 8% strand | P00953 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
- AMP · Adenosine monophosphate · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
- PO4 · Phosphate ion · ion · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.79 | 0.81 | 117 | TRP, PO4, AMP |
| 2 | 800 | 0.74 | 0.79 | 58 | TRP, PO4, AMP |
| 3 | 743 | 0.74 | 0.79 | 79 | empty |
| 4 | 787 | 0.74 | 0.79 | 58 | TRP, PO4, AMP |
| 5 | 927 | 0.73 | 0.77 | 70 | TRP, PO4, AMP |
Interfaces
26 interfaces between chains.
- H–K · 2206 Ų buried · 39 hydrogen bonds · protein-protein
- G–J · 2200 Ų buried · 36 hydrogen bonds · protein-protein
- I–L · 2192 Ų buried · 36 hydrogen bonds · protein-protein
- N–Q · 2186 Ų buried · 35 hydrogen bonds · protein-protein
- O–R · 2182 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 180 modified (engineered).
Compared structures
- 3FI0 · Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase… · the same entry in another collection · chain J against J, 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 P00953
- Elsewhere: RCSB PDB 3FI0 · PDBe 3FI0 · UniProt P00953
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