MolNFT v1 · #159721 · protein
Escherichia COLI tRNA synthetase in complex with compound 3
6OZ5 · Phenylalanine--tRNA ligase alpha subunit: “Escherichia COLI tRNA synthetase in complex with compound 3”. X-ray diffraction, 2 ligands (VB3, MG), 20 pockets (best druggability 0.81). MolNFT v1 #159721 on GenesisL1: 3D structure…
- PDB
- 6OZ5
- 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
- VB3, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 241 | 32% helix, 28% strand | A0A387D3L6 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 793 | 26% helix, 29% strand | A0A387D0Y5 |
| C | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 322 | 44% helix, 19% strand | A0A387D3L6 |
| D | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 794 | 26% helix, 29% strand | A0A387D0Y5 |
Ligands and binding sites
- VB3 · 2-({[(2S)-1-cyclohexylpropan-2-yl]amino}methyl)phenol · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PGE · Triethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.81 | 0.84 | 94 | EDO |
| 2 | 375 | 0.77 | 0.87 | 32 | EDO |
| 3 | 856 | 0.77 | 0.80 | 76 | VB3, PGE |
| 4 | 758 | 0.76 | 0.80 | 69 | VB3 |
| 5 | 277 | 0.74 | 0.87 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3710 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3657 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 1992 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1911 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1310 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6OZ5 · Escherichia coli tRNA synthetase in complex with compound 3 · 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 A0A387D3L6
- Every structure of UniProt A0A387D0Y5
- Elsewhere: RCSB PDB 6OZ5 · PDBe 6OZ5 · UniProt A0A387D3L6 · UniProt A0A387D0Y5
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