Research workbench
Sirohydrochlorin-bound S. typhimurium siroheme synthase
Analyse 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
- 6P5X
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siroheme synthase
- EC
- 2.1.1.107
- UniProt
- A0A3V0JC15
- Ligands
- SAH, SHN, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Siroheme synthase (EC 2.1.1.107) | protein | 451 | 39% helix, 22% strand | A0A3V0JC15 |
| B | Siroheme synthase (EC 2.1.1.107) | protein | 449 | 41% helix, 22% strand | A0A3V0JC15 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SHN · 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid · ligand · 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.79 | 0.81 | 72 | SHN |
| 2 | 645 | 0.73 | 0.80 | 67 | SAH, CL |
| 3 | 581 | 0.71 | 0.79 | 68 | SAH |
| 4 | 150 | 0.65 | 0.86 | 20 | empty |
| 5 | 210 | 0.58 | 0.80 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 6468 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
- 6P5X · 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 6P5X · PDBe 6P5X · UniProt A0A3V0JC15
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