Research workbench
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
- 3LMU
- Type
- protein
- Length
- 1,184 residues
- Chains
- 8
- 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
- 15 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 155 | 23% helix, 37% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 148 | 26% helix, 42% strand | Q8IIS0 |
| C, D, G, H | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 148 | 24% helix, 39% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 145 | 24% helix, 41% strand | Q8IIS0 |
| F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 144 | 24% helix, 38% strand | Q8IIS0 |
Ligands and binding sites
- IOD · Iodide ion · ion · 26 copies · chains A, B, C, D, E, F, G, H
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 | 811 | 0.69 | 0.75 | 64 | IOD |
| 2 | 624 | 0.67 | 0.77 | 44 | IOD |
| 3 | 541 | 0.65 | 0.76 | 53 | IOD |
| 4 | 204 | 0.59 | 0.81 | 37 | IOD |
| 5 | 135 | 0.54 | 0.81 | 29 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1857 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1811 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 1788 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1762 Ų buried · 43 hydrogen bonds · protein-protein
- E–H · 232 Ų buried · 0 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 3LMU · PDBe 3LMU · UniProt Q8IIS0
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