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The crystal structure of desulfovibrio vulgaris dissimilatory sulfite reductase bound to dsrc provides novel insights into the mechanism of sulfate respiration
Analyse The crystal structure of desulfovibrio vulgaris dissimilatory sulfite reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V4J
- Type
- protein
- Length
- 1,838 residues
- Chains
- 6
- 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
- P45574, P45575, P45573
- Ligands
- SF4, SH0, SRM, SO3
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sulfite reductase, dissimilatory-type subunit alpha (EC 1.8.99.3) | protein | 436 | 36% helix, 14% strand | P45574 |
| B, E | Sulfite reductase, dissimilatory-type subunit beta (EC 1.8.99.3) | protein | 380 | 31% helix, 22% strand | P45575 |
| C, F | Sulfite reductase, dissimilatory-type subunit gamma (EC 1.8.99.3) | protein | 103 | 54% helix, 8% strand | P45573 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, D, E
- SH0 · 3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,11S,12S,13S,16S,19S)-3,8,13,17-tetrakis(carboxylatomethyl)-8,13-dimethyl-1,2,3,4,7,8,11,12,13,16,19,20,22,24-tetradecahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoate · ligand · 2 copies · chains A, B, D, E
- SRM · Siroheme · ligand · 2 copies · chains A, B, C, D, E, F
- SO3 · Sulfite ion · ion · 2 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.88 | 0.93 | 61 | SF4, SH0 |
| 2 | 628 | 0.88 | 0.93 | 64 | SF4, SH0 |
| 3 | 575 | 0.87 | 0.93 | 84 | SF4, SRM, SO3 |
| 4 | 417 | 0.85 | 0.93 | 53 | SF4, SRM, SO3 |
| 5 | 542 | 0.82 | 0.88 | 64 | empty |
Interfaces
12 interfaces between chains.
- A–B · 6401 Ų buried · 122 hydrogen bonds · protein-protein
- D–E · 6382 Ų buried · 117 hydrogen bonds · protein-protein
- A–E · 3088 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 3088 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 1014 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 2V4J · THE CRYSTAL STRUCTURE OF Desulfovibrio vulgaris DISSIMILATORY SULFITE REDUCTASE BOUND TO… · the same entry in another collection · chain C against C, TM-score 1.00
- P45574 · AlphaFold monomer V2.0 prediction for sulfite reductase, dissimilatory-type subunit alpha… · a predicted model of the same protein · chain D against A, TM-score 1.00
- P45575 · 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 1.00
- P45573 · AlphaFold monomer V2.0 prediction for sulfite reductase, dissimilatory-type subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P45574
- Every structure of UniProt P45575
- Every structure of UniProt P45573
- Elsewhere: RCSB PDB 2V4J · PDBe 2V4J · UniProt P45574 · UniProt P45575 · UniProt P45573
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