Research workbench
WELO5 small molecule halogenase with NI(II) and succinate
Analyse WELO5 small molecule halogenase with NI(II) and succinate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TRQ
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WELO5
- UniProt
- A0A067YX61
- Ligands
- NI, CA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | WELO5 | protein | 283 | 30% helix, 27% strand | A0A067YX61 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.71 | 0.82 | 45 | NI, SIN |
| 2 | 378 | 0.70 | 0.82 | 46 | NI, SIN |
| 3 | 164 | 0.53 | 0.79 | 28 | empty |
| 4 | 55 | 0.47 | 0.85 | 15 | empty |
| 5 | 84 | 0.40 | 0.78 | 31 | CA |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5TRQ · WELO5 small molecule halogenase with NI(II) and succinate · 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 A0A067YX61
- Elsewhere: RCSB PDB 5TRQ · PDBe 5TRQ · UniProt A0A067YX61
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