MolNFT v1 · #69907 · protein
Crystal structure of homo sapiens cytoplasmic phenylalanyl-tRNA synthetase
3L4G · Phenylalanyl-tRNA synthetase alpha chain: “Crystal structure of homo sapiens cytoplasmic phenylalanyl-tRNA synthetase”. X-ray diffraction, 1 ligand (PHE), 20 pockets (best druggability 0.86). MolNFT v1 #69907 on GenesisL1: 3D…
- PDB
- 3L4G
- Type
- protein
- Length
- 7,448 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase alpha chain; Phenylalanyl-tRNA synthetase beta chain
- EC
- 6.1.1.20
- UniProt
- Q9Y285, Q9NSD9
- Ligands
- PHE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 318 | 26% helix, 20% strand | Q9Y285 |
| B, D, F, H, J, L, N, P | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 589 | 28% helix, 27% strand | Q9NSD9 |
| C | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 508 | 34% helix, 18% strand | Q9Y285 |
| E | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 309 | 28% helix, 19% strand | Q9Y285 |
| G, O | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 309 | 27% helix, 21% strand | Q9Y285 |
| I | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 313 | 30% helix, 21% strand | Q9Y285 |
| K | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 349 | 31% helix, 18% strand | Q9Y285 |
| M | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 321 | 27% helix, 19% strand | Q9Y285 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 8 copies · chains A, C, E, G, I, K, M, O
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 | 539 | 0.86 | 0.92 | 59 | empty |
| 2 | 528 | 0.85 | 0.92 | 61 | empty |
| 3 | 486 | 0.85 | 0.92 | 56 | empty |
| 4 | 332 | 0.84 | 0.94 | 44 | empty |
| 5 | 953 | 0.82 | 0.83 | 95 | PHE |
Interfaces
48 interfaces between chains.
- E–F · 4509 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 4438 Ų buried · 57 hydrogen bonds · protein-protein
- I–J · 4379 Ų buried · 50 hydrogen bonds · protein-protein
- O–P · 4371 Ų buried · 56 hydrogen bonds · protein-protein
- M–N · 4352 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 3L4G · Crystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA synthetase · the same entry in another collection · chain G against G, 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 Q9Y285
- Every structure of UniProt Q9NSD9
- Elsewhere: RCSB PDB 3L4G · PDBe 3L4G · UniProt Q9Y285 · UniProt Q9NSD9
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