Research workbench
Dtd from plasmodium falciparum in complex with D-histidine
Analyse Dtd from plasmodium falciparum in complex with D-histidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KOC
- Type
- protein
- Length
- 906 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
- DHI
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 153 | 24% helix, 42% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 149 | 23% helix, 43% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 159 | 24% helix, 36% strand | Q8IIS0 |
| D | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 45% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 147 | 26% helix, 42% strand | Q8IIS0 |
| F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 148 | 24% helix, 41% strand | Q8IIS0 |
Ligands and binding sites
- DHI · D-histidine · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.69 | 0.83 | 44 | empty |
| 2 | 235 | 0.59 | 0.80 | 32 | empty |
| 3 | 145 | 0.52 | 0.80 | 29 | empty |
| 4 | 210 | 0.52 | 0.77 | 32 | empty |
| 5 | 157 | 0.51 | 0.79 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1890 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1799 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1786 Ų buried · 43 hydrogen bonds · protein-protein
- A–F · 708 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 495 Ų buried · 7 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 3KOC · PDBe 3KOC · UniProt Q8IIS0
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