Research workbench
Crystal structure of dissimilatory sulfite reductase II (dsrii)
Analyse Crystal structure of dissimilatory sulfite reductase II (dsrii) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OR2
- Type
- protein
- Length
- 1,848 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfite redcutase subunit alpha; Sulfite redcutase subunit beta; Sulfite redcutase…
- Ligands
- SF4, SRM, SO3
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sulfite redcutase subunit alpha | protein | 435 | 37% helix, 14% strand | — |
| B, E | Sulfite redcutase subunit beta | protein | 385 | 30% helix, 21% strand | — |
| C, F | Sulfite redcutase subunit gama | protein | 104 | 53% helix, 10% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, D, E
- SRM · Siroheme · ligand · 4 copies · chains A, B, C, D, E, F
- SO3 · Sulfite ion · ion · 4 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.89 | 0.92 | 99 | SRM, SO3, SF4 |
| 2 | 1136 | 0.88 | 0.90 | 136 | SO3, SRM, SF4 |
| 3 | 668 | 0.88 | 0.92 | 70 | SF4, SRM |
| 4 | 656 | 0.87 | 0.92 | 66 | SF4, SRM |
| 5 | 706 | 0.80 | 0.84 | 86 | empty |
Interfaces
12 interfaces between chains.
- D–E · 6320 Ų buried · 110 hydrogen bonds · protein-protein
- A–B · 6261 Ų buried · 110 hydrogen bonds · protein-protein
- A–E · 3160 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 3129 Ų buried · 45 hydrogen bonds · protein-protein
- D–F · 1026 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3OR2 · Crystal structure of dissimilatory sulfite reductase II (DsrII) · 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
- Elsewhere: RCSB PDB 3OR2 · PDBe 3OR2
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