Research workbench
Dtd from plasmodium falciparum in complex with D-serine
Analyse Dtd from plasmodium falciparum in complex with D-serine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KOD
- Type
- protein
- Length
- 912 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
- DSN
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 23% helix, 41% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 157 | 25% helix, 38% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 155 | 26% helix, 40% 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 | 147 | 27% helix, 37% strand | Q8IIS0 |
Ligands and binding sites
- DSN · D-serine · ligand · 4 copies · chains B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.72 | 0.82 | 52 | empty |
| 2 | 200 | 0.55 | 0.79 | 33 | empty |
| 3 | 180 | 0.52 | 0.78 | 29 | empty |
| 4 | 170 | 0.52 | 0.78 | 29 | empty |
| 5 | 112 | 0.51 | 0.81 | 21 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1864 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 1858 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1851 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 667 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 5 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 3KOD · PDBe 3KOD · UniProt Q8IIS0
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