Research workbench
Crystal structure of pyrrolysyl-tRNA synthetase (N346D/C348S/Y384F) in complex with O-chlorophenylalanine and AMP-pnp
Analyse Crystal structure of pyrrolysyl-tRNA synthetase (N346D/C348S/Y384F) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RSM
- Type
- protein
- Length
- 1,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase
- EC
- 6.1.1.26
- UniProt
- A0A0F8JXW8
- Ligands
- ANP, 2L5
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 267 | 39% helix, 22% strand | A0A0F8JXW8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- 2L5 · 2-chloro-L-phenylalanine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.69 | 0.81 | 39 | ANP, 2L5 |
| 2 | 405 | 0.69 | 0.81 | 41 | ANP, 2L5 |
| 3 | 419 | 0.69 | 0.80 | 40 | ANP, 2L5 |
| 4 | 411 | 0.68 | 0.80 | 41 | ANP, 2L5 |
| 5 | 438 | 0.58 | 0.74 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2611 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 174 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 123 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RSM · Crystal structure of pyrrolysyl-tRNA synthetase (N346D/C348S/Y384F) in complex with… · 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 A0A0F8JXW8
- Elsewhere: RCSB PDB 7RSM · PDBe 7RSM · UniProt A0A0F8JXW8
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