MolNFT v1 · #169761 · protein
Crystal structure of iron-bound LSD4 from sphingobium sp. strain syk-6
6XMA · Dioxygenase: “Crystal structure of iron-bound LSD4 from sphingobium sp. strain syk-6”. X-ray diffraction, 2 ligands (FE, SO4), 5 pockets (best druggability 0.74). MolNFT v1 #169761 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XMA
- Type
- protein
- Length
- 479 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase
- EC
- 1.13.11.-
- UniProt
- G2IQT9
- Ligands
- FE, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase (EC 1.13.11.-) | protein | 479 | 9% helix, 40% strand | G2IQT9 |
Ligands and binding sites
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 | 427 | 0.74 | 0.84 | 46 | empty |
| 2 | 478 | 0.70 | 0.80 | 43 | SO4 |
| 3 | 56 | 0.67 | 0.96 | 25 | empty |
| 4 | 122 | 0.48 | 0.79 | 23 | empty |
| 5 | 70 | 0.34 | 0.76 | 15 | empty |
Compared structures
- 6XMA · Crystal structure of iron-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 6XMA · PDBe 6XMA · UniProt G2IQT9
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