MolNFT v1 · #103950 · protein
Crystal structure of the sulfite dehydrogenase sort from sinorhizobium meliloti
4PW3 · Putative sulfite oxidase: “Crystal structure of the sulfite dehydrogenase sort from sinorhizobium meliloti”. X-ray diffraction, 1 ligand (MSS), 20 pockets (best druggability 0.76). MolNFT v1 #103950 on GenesisL1: 3D structure…
- PDB
- 4PW3
- Type
- protein
- Length
- 1,458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sulfite oxidase
- EC
- 1.8.3.1
- UniProt
- Q92M24
- Ligands
- MSS
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Putative sulfite oxidase (EC 1.8.3.1) | protein | 365 | 13% helix, 36% strand | Q92M24 |
| B | Putative sulfite oxidase (EC 1.8.3.1) | protein | 363 | 13% helix, 36% strand | Q92M24 |
Ligands and binding sites
- MSS · (molybdopterin-S,S)-oxo-molybdenum · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.76 | 0.99 | 23 | MSS |
| 2 | 82 | 0.76 | 0.98 | 22 | MSS |
| 3 | 75 | 0.73 | 0.97 | 22 | MSS |
| 4 | 1023 | 0.73 | 0.76 | 91 | empty |
| 5 | 70 | 0.72 | 0.97 | 22 | MSS |
Interfaces
4 interfaces between chains.
- C–D · 1322 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1316 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PW3 · Crystal structure of the sulfite dehydrogenase SorT from Sinorhizobium meliloti · 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 Q92M24
- Elsewhere: RCSB PDB 4PW3 · PDBe 4PW3 · UniProt Q92M24
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