Research workbench
Cryo-EM structure of sulfur oxygenase reductase from sulfurisphaera tokodaii
Analyse Cryo-EM structure of sulfur oxygenase reductase from sulfurisphaera tokodaii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M3X
- Type
- protein
- Length
- 7,440 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfur OXYGENASE/REDUCTASE
- EC
- 1.13.11.55
- UniProt
- Q972K4
- Ligands
- FE
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Sulfur OXYGENASE/REDUCTASE (EC 1.13.11.55) | protein | 310 | 36% helix, 31% strand | Q972K4 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.88 | 0.91 | 60 | empty |
| 2 | 784 | 0.88 | 0.91 | 60 | empty |
| 3 | 793 | 0.88 | 0.91 | 60 | empty |
| 4 | 793 | 0.88 | 0.90 | 60 | empty |
| 5 | 785 | 0.88 | 0.90 | 60 | empty |
Interfaces
72 interfaces between chains.
- C–E · 2734 Ų buried · 55 hydrogen bonds · protein-protein
- R–W · 2734 Ų buried · 55 hydrogen bonds · protein-protein
- B–X · 2731 Ų buried · 55 hydrogen bonds · protein-protein
- G–U · 2731 Ų buried · 55 hydrogen bonds · protein-protein
- D–Q · 2730 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 6M3X · Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii · 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 Q972K4
- Elsewhere: RCSB PDB 6M3X · PDBe 6M3X · UniProt Q972K4
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