Research workbench
Crystal structure of sphingomonas paucimobilis TMY1009 holo-lsda
Analyse Crystal structure of sphingomonas paucimobilis TMY1009 holo-lsda in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OJW
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lignostilbene-ALPHA,BETA-dioxygenase isozyme I
- EC
- 1.13.11.43
- UniProt
- Q53353
- Ligands
- FE, MG
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Lignostilbene-ALPHA,BETA-dioxygenase isozyme I (EC 1.13.11.43) | protein | 464 | 9% helix, 40% strand | Q53353 |
| A | Lignostilbene-ALPHA,BETA-dioxygenase isozyme I (EC 1.13.11.43) | protein | 480 | 9% helix, 39% strand | Q53353 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains B, A
- MG · Magnesium ion · metal · chains B, A
- GOL · Glycerol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.82 | 0.92 | 47 | empty |
| 2 | 96 | 0.75 | 0.97 | 27 | empty |
| 3 | 327 | 0.72 | 0.85 | 51 | empty |
| 4 | 422 | 0.66 | 0.79 | 55 | empty |
| 5 | 211 | 0.59 | 0.80 | 40 | empty |
Interfaces
1 interface between chains.
- B–A · 1536 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6OJW · Crystal structure of Sphingomonas paucimobilis TMY1009 holo-LsdA · the same entry in another collection · chain B against B, TM-score 1.00
- Q53353 · AlphaFold monomer V2.0 prediction for lignostilbene-ALPHA,BETA- dioxygenase isozyme I… · a predicted model of the same protein · chain B 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 Q53353
- Elsewhere: RCSB PDB 6OJW · PDBe 6OJW · UniProt Q53353
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