Research workbench
Crystal structure of cobalt-bound LSD4 from sphingobium sp. strain syk-6
Analyse Crystal structure of cobalt-bound LSD4 from sphingobium sp. strain syk-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XM6
- Type
- protein
- Length
- 484 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase
- EC
- 1.13.11.-
- UniProt
- G2IQT9
- Ligands
- CO
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase (EC 1.13.11.-) | protein | 484 | 9% helix, 39% strand | G2IQT9 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.76 | 0.85 | 45 | empty |
| 2 | 414 | 0.73 | 0.83 | 46 | empty |
| 3 | 125 | 0.48 | 0.79 | 21 | empty |
| 4 | 58 | 0.31 | 0.75 | 14 | empty |
Compared structures
- 6XM6 · Crystal structure of cobalt-bound LSD4 from Sphingobium sp. strain SYK-6 · 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 G2IQT9
- Elsewhere: RCSB PDB 6XM6 · PDBe 6XM6 · UniProt G2IQT9
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