MolNFT v1 · #40459 · protein
Crystal structure of a putative tRNA-(MS(2)IO(6)A)-hydroxylase (PP_2188) from pseudomonas putida KT2440 at 2.05 a resolution
2ITB · TRNA-(MS(2)IO(6)A)-hydroxylase, putative: “Crystal structure of a putative tRNA-(MS(2)IO(6)A)-hydroxylase (PP_2188) from pseudomonas putida KT2440 at…”. X-ray diffraction, 3 ligands (UNL, FE, PER), 3 pockets (best druggability…
- PDB
- 2ITB
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-(MS(2)IO(6)A)-hydroxylase, putative
- UniProt
- Q88KV1
- Ligands
- UNL, FE, PER
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-(MS(2)IO(6)A)-hydroxylase, putative | protein | 199 | 73% helix, 2% strand | Q88KV1 |
| B | TRNA-(MS(2)IO(6)A)-hydroxylase, putative | protein | 198 | 72% helix, 1% strand | Q88KV1 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- PER · Peroxide ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.71 | 0.84 | 54 | UNL, EDO |
| 2 | 222 | 0.70 | 0.86 | 38 | PER, EDO |
| 3 | 51 | 0.37 | 0.80 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2ITB · Crystal structure of a putative tRNA-(MS(2)IO(6)A)-hydroxylase (PP_2188) from pseudomonas… · 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 Q88KV1
- Elsewhere: RCSB PDB 2ITB · PDBe 2ITB · UniProt Q88KV1
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