MolNFT v1 · #160668 · protein
D262A/S128A S. typhimurium siroheme synthase
6PR3: “D262A/S128A S. typhimurium siroheme synthase”. X-ray diffraction, 2 ligands (SAH, CL), 11 pockets (best druggability 0.75). MolNFT v1 #160668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PR3
- Type
- protein
- Length
- 898 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
- A0A0F7JCI1
- Ligands
- SAH, CL
- Pockets
- 11 · best druggability 0.75
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, 1.3.1.76, 4.99.1.4) | protein | 450 | 40% helix, 22% strand | A0A0F7JCI1 |
| B | Siroheme synthase (EC 2.1.1.107, 1.3.1.76, 4.99.1.4) | protein | 448 | 41% helix, 22% strand | A0A0F7JCI1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.75 | 0.80 | 48 | CL |
| 2 | 459 | 0.75 | 0.84 | 45 | empty |
| 3 | 546 | 0.72 | 0.80 | 58 | SAH |
| 4 | 592 | 0.71 | 0.79 | 68 | SAH |
| 5 | 133 | 0.53 | 0.81 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 6288 Ų buried · 80 hydrogen bonds · protein-protein
Compared structures
- 6PR3 · D262A/S128A 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 A0A0F7JCI1
- Elsewhere: RCSB PDB 6PR3 · PDBe 6PR3 · UniProt A0A0F7JCI1
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