Research workbench
Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase
Analyse Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P5Z
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siroheme synthase
- EC
- 2.1.1.107, 1.3.1.76, 4.99.1.4
- UniProt
- A0A3V0JC15
- Ligands
- SAH, F0X, CL
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Siroheme synthase (EC 2.1.1.107, 1.3.1.76, 4.99.1.4) | protein | 450 | 38% helix, 21% strand | A0A3V0JC15 |
| B | Siroheme synthase (EC 2.1.1.107, 1.3.1.76, 4.99.1.4) | protein | 446 | 39% helix, 22% strand | A0A3V0JC15 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- F0X · cobalt-sirohydrochlorin · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.77 | 0.81 | 57 | CL |
| 2 | 766 | 0.75 | 0.80 | 71 | SAH, F0X, CL |
| 3 | 387 | 0.70 | 0.82 | 45 | SAH |
| 4 | 342 | 0.70 | 0.83 | 36 | empty |
| 5 | 232 | 0.62 | 0.82 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 6392 Ų buried · 78 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P5Z · Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase · 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 A0A3V0JC15
- Elsewhere: RCSB PDB 6P5Z · PDBe 6P5Z · UniProt A0A3V0JC15
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