MolNFT v1 · #14494 · protein
Crystal structure of tryptophanyl-tRNA synthetase complexed with tryptophan in an open conformation
1MB2 · Tryptophan-tRNA ligase: “Crystal structure of tryptophanyl-tRNA synthetase complexed with tryptophan in an open conformation”. X-ray diffraction, 1 ligand (TRP), 15 pockets (best druggability 0.75). MolNFT v1 #14494 on GenesisL1: 3D…
- PDB
- 1MB2
- Type
- protein
- Length
- 1,956 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan-tRNA ligase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- TRP
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tryptophan-tRNA ligase (EC 6.1.1.2) | protein | 326 | 57% helix, 9% strand | P00953 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.75 | 0.81 | 57 | TRP |
| 2 | 667 | 0.75 | 0.80 | 55 | TRP |
| 3 | 680 | 0.74 | 0.80 | 53 | TRP |
| 4 | 611 | 0.74 | 0.81 | 52 | TRP |
| 5 | 661 | 0.74 | 0.80 | 51 | TRP |
Interfaces
4 interfaces between chains.
- C–F · 2176 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2154 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 2134 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 377 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1MB2 · Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open… · the same entry in another collection · chain E against E, TM-score 1.00
- P00953 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P00953) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P00953
- Elsewhere: RCSB PDB 1MB2 · PDBe 1MB2 · UniProt P00953
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