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Crystal structure of dtd from plasmodium falciparum
Analyse Crystal structure of dtd from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMT
- Type
- protein
- Length
- 928 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tyrosyl-TRNA(TYR) deacylase
- EC
- 3.1.-.-
- UniProt
- Q8IIS0
- Ligands
- IOD
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 162 | 23% helix, 44% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 23% helix, 38% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 161 | 24% helix, 41% strand | Q8IIS0 |
| D | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 41% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 43% strand | Q8IIS0 |
| F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 23% helix, 43% strand | Q8IIS0 |
Ligands and binding sites
- IOD · Iodide ion · ion · 29 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.75 | 0.80 | 90 | IOD |
| 2 | 246 | 0.61 | 0.80 | 29 | IOD |
| 3 | 224 | 0.60 | 0.81 | 32 | IOD |
| 4 | 200 | 0.58 | 0.80 | 33 | IOD |
| 5 | 155 | 0.52 | 0.80 | 28 | IOD |
Interfaces
10 interfaces between chains.
- A–B · 1944 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 1864 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1797 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 229 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 209 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q8IIS0
- Elsewhere: RCSB PDB 3LMT · PDBe 3LMT · UniProt Q8IIS0
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