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Crystal structure of a putative 2,3-dioxygenase (SO4414) from shewanella oneidensis in complex with ferric heme. northeast structural genomics target SOR52.
Analyse Crystal structure of a putative 2,3-dioxygenase (SO4414) from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NWB
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved domain protein
- UniProt
- Q8E972
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved domain protein | protein | 379 | 68% helix, 3% strand | Q8E972 |
| B | Conserved domain protein | protein | 365 | 64% helix, 3% strand | Q8E972 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.80 | 0.83 | 61 | HEM |
| 2 | 1049 | 0.79 | 0.80 | 85 | empty |
| 3 | 617 | 0.77 | 0.83 | 59 | empty |
| 4 | 406 | 0.68 | 0.80 | 43 | empty |
| 5 | 88 | 0.51 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1394 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2NWB · Crystal Structure of a Putative 2,3-dioxygenase (SO4414) from Shewanella oneidensis in… · 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 Q8E972
- Elsewhere: RCSB PDB 2NWB · PDBe 2NWB · UniProt Q8E972
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