Research workbench
Dissimilatory sulfite reductase nitrite complex
Analyse Dissimilatory sulfite reductase nitrite complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MM9
- Type
- protein
- Length
- 1,560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfite reductase, dissimilatory-type subunit alpha; Sulfite reductase…
- EC
- 1.8.99.3
- UniProt
- Q59109, Q59110
- Ligands
- SF4, SRM, NO2
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sulfite reductase, dissimilatory-type subunit alpha (EC 1.8.99.3) | protein | 417 | 39% helix, 17% strand | Q59109 |
| B, E | Sulfite reductase, dissimilatory-type subunit beta (EC 1.8.99.3) | protein | 363 | 33% helix, 21% strand | Q59110 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, D, E
- SRM · Siroheme · ligand · 4 copies · chains A, B, D, E
- NO2 · Nitrite ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.86 | 0.94 | 51 | SF4, SRM |
| 2 | 426 | 0.86 | 0.94 | 65 | SF4, SRM |
| 3 | 826 | 0.80 | 0.83 | 65 | SRM, SF4 |
| 4 | 746 | 0.79 | 0.83 | 63 | SRM, NO2, SF4 |
| 5 | 1159 | 0.76 | 0.79 | 69 | empty |
Interfaces
6 interfaces between chains.
- D–E · 6453 Ų buried · 96 hydrogen bonds · protein-protein
- A–B · 6421 Ų buried · 111 hydrogen bonds · protein-protein
- A–E · 2042 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2030 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 1091 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3MM9 · Dissimilatory sulfite reductase nitrite complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q59109 · AlphaFold monomer V2.0 prediction for sulfite reductase, dissimilatory-type subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q59110 · AlphaFold monomer V2.0 prediction for sulfite reductase, dissimilatory-type subunit beta… · a predicted model of the same protein · chain E against A, TM-score 0.96
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 Q59109
- Every structure of UniProt Q59110
- Elsewhere: RCSB PDB 3MM9 · PDBe 3MM9 · UniProt Q59109 · UniProt Q59110
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