MolNFT v1 · #159987 · protein
D104N S. typhimurium siroheme synthase
6P7D: “D104N S. typhimurium siroheme synthase”. X-ray diffraction, 2 ligands (SAH, CL), 11 pockets (best druggability 0.84). MolNFT v1 #159987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P7D
- Type
- protein
- Length
- 894 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, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 447 | 39% helix, 22% strand | A0A3V0JC15 |
| B | Siroheme synthase (EC 2.1.1.107, 1.3.1.76, 4.99.1.4) | protein | 447 | 40% helix, 22% strand | A0A3V0JC15 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.84 | 0.85 | 111 | SAH |
| 2 | 979 | 0.76 | 0.79 | 81 | CL |
| 3 | 422 | 0.68 | 0.80 | 45 | SAH |
| 4 | 212 | 0.54 | 0.77 | 32 | empty |
| 5 | 205 | 0.49 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 6229 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 6P7D · D104N 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 6P7D · PDBe 6P7D · UniProt A0A3V0JC15
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