MolNFT v1 · #51338 · protein
The crystal structure of desulfovibrio vulgaris dissimilatory sulfite reductase bound to dsrc provides novel insights into the mechanism of sulfate respiration
2V4J · Sulfite reductase, dissimilatory-type subunit alpha: “The crystal structure of desulfovibrio vulgaris dissimilatory sulfite reductase bound to dsrc provides novel…”. X-ray diffraction, 4 ligands (SF4, SH0, SRM), 17 pockets (best…
- 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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