MolNFT v1 · #82558 · protein
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with amppnp (re-refined)
3VQV · Pyrrolysine--tRNA ligase: “Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with amppnp (re-refined)”. X-ray diffraction, 2 ligands (ANP, MG), 3 pockets (best druggability 0.69). MolNFT v1 #82558 on…
- PDB
- 3VQV
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase
- EC
- 6.1.1.26
- Ligands
- ANP, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 258 | 39% helix, 23% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.69 | 0.81 | 42 | ANP, MG |
| 2 | 95 | 0.35 | 0.74 | 19 | empty |
| 3 | 54 | 0.28 | 0.75 | 12 | empty |
Compared structures
- 3VQV · Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase 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
- Elsewhere: RCSB PDB 3VQV · PDBe 3VQV
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