MolNFT v1 · #159824 · protein
Escherichia COLI tRNA synthetase in complex with compound 1
6P26 · Phenylalanine--tRNA ligase alpha subunit: “Escherichia COLI tRNA synthetase in complex with compound 1”. X-ray diffraction, 1 ligand (NO4), 20 pockets (best druggability 0.79). MolNFT v1 #159824 on GenesisL1: 3D structure, binding…
- PDB
- 6P26
- Type
- protein
- Length
- 2,150 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine--tRNA ligase alpha subunit; Phenylalanine--tRNA ligase beta subunit
- EC
- 6.1.1.20
- UniProt
- A0A387D3L6, A0A387D0Y5
- Ligands
- NO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 241 | 31% helix, 27% strand | A0A387D3L6 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 793 | 26% helix, 28% strand | A0A387D0Y5 |
| C | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 322 | 42% helix, 19% strand | A0A387D3L6 |
| D | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 794 | 28% helix, 29% strand | A0A387D0Y5 |
Ligands and binding sites
- NO4 · N-benzyl-2-(cyclohex-1-en-1-yl)ethan-1-amine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.79 | 0.86 | 49 | empty |
| 2 | 540 | 0.78 | 0.85 | 51 | empty |
| 3 | 1109 | 0.78 | 0.80 | 80 | empty |
| 4 | 365 | 0.77 | 0.87 | 31 | empty |
| 5 | 844 | 0.76 | 0.80 | 77 | NO4 |
Interfaces
6 interfaces between chains.
- C–D · 3781 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3694 Ų buried · 66 hydrogen bonds · protein-protein
- B–C · 2054 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1960 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1328 Ų buried · 31 hydrogen bonds · protein-protein
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 A0A387D3L6
- Every structure of UniProt A0A387D0Y5
- Elsewhere: RCSB PDB 6P26 · PDBe 6P26 · UniProt A0A387D3L6 · UniProt A0A387D0Y5
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