MolNFT v1 · #61163 · protein
Crystal structure of a domain of unknown function with a heme oxygenase-like fold (SDEN_3740) from shewanella denitrificans OS217 at 2.30 a resolution
3DDE · TENA/THI-4 protein, domain of unknown function with a heme…: “Crystal structure of a domain of unknown function with a heme oxygenase-like fold (SDEN_3740) from shewanella…”. X-ray diffraction, 1 ligand (NO3), 5 pockets (best…
- PDB
- 3DDE
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TENA/THI-4 protein, domain of unknown function with a heme oxygenase-like fold
- UniProt
- Q12HR3
- Ligands
- NO3
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TENA/THI-4 protein, domain of unknown function with a heme oxygenase-like fold | protein | 232 | 78% helix, 0% strand | Q12HR3 |
| B | TENA/THI-4 protein, domain of unknown function with a heme oxygenase-like fold | protein | 231 | 77% helix, 0% strand | Q12HR3 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- PGE · Triethylene glycol · additive · 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 | 418 | 0.83 | 0.90 | 54 | NO3, PGE |
| 2 | 298 | 0.82 | 0.92 | 49 | empty |
| 3 | 68 | 0.56 | 0.88 | 20 | empty |
| 4 | 88 | 0.36 | 0.75 | 19 | empty |
| 5 | 93 | 0.35 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3DDE · Crystal structure of a domain of unknown function with a heme oxygenase-like fold… · 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 Q12HR3
- Elsewhere: RCSB PDB 3DDE · PDBe 3DDE · UniProt Q12HR3
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