MolNFT v1 · #160039 · protein
Acinetobacter baumannii tRNA synthetase in complex with compound 1
6P8T · Phenylalanine--tRNA ligase beta subunit: “Acinetobacter baumannii tRNA synthetase in complex with compound 1”. X-ray diffraction, 2 ligands (NO4, MG), 20 pockets (best druggability 0.86). MolNFT v1 #160039 on GenesisL1: 3D…
- PDB
- 6P8T
- Type
- protein
- Length
- 3,994 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine--tRNA ligase beta subunit; Phenylalanine--tRNA ligase alpha subunit
- EC
- 6.1.1.20
- UniProt
- D0CA71, D0CA72
- Ligands
- NO4, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 792 | 26% helix, 26% strand | D0CA71 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 777 | 27% helix, 27% strand | D0CA71 |
| C | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 320 | 43% helix, 20% strand | D0CA72 |
| D | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 231 | 29% helix, 29% strand | D0CA72 |
| E | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 793 | 26% helix, 29% strand | D0CA71 |
| F | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 463 | 30% helix, 27% strand | D0CA71 |
| G | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 292 | 39% helix, 23% strand | D0CA72 |
| H | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 326 | 43% helix, 20% strand | D0CA72 |
Ligands and binding sites
- NO4 · N-benzyl-2-(cyclohex-1-en-1-yl)ethan-1-amine · ligand · 4 copies · chains C, D, G, H
- MG · Magnesium ion · metal · 3 copies · chains A, C, B, D, E, G
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 | 986 | 0.86 | 0.88 | 86 | empty |
| 2 | 1027 | 0.86 | 0.87 | 96 | empty |
| 3 | 647 | 0.75 | 0.81 | 78 | NO4 |
| 4 | 450 | 0.75 | 0.84 | 37 | empty |
| 5 | 981 | 0.75 | 0.78 | 72 | empty |
Interfaces
18 interfaces between chains.
- E–G · 3429 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 3400 Ų buried · 45 hydrogen bonds · protein-protein
- F–H · 3286 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 3280 Ų buried · 50 hydrogen bonds · protein-protein
- F–G · 2123 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6P8T · Acinetobacter baumannii tRNA synthetase in complex with compound 1 · 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 D0CA71
- Every structure of UniProt D0CA72
- Elsewhere: RCSB PDB 6P8T · PDBe 6P8T · UniProt D0CA71 · UniProt D0CA72
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