Research workbench
Precorrin-2-bound S128A S. typhimurium siroheme synthase
Analyse Precorrin-2-bound S128A 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
- 6VEB
- 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, 1.3.1.76, 4.99.1.4
- UniProt
- A0A3U8X2F7
- Ligands
- SAH, NAD, PQ2, CL
- Pockets
- 10 · best druggability 0.80
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 | 451 | 39% helix, 22% strand | A0A3U8X2F7 |
| B | Siroheme synthase (EC 2.1.1.107, 1.3.1.76, 4.99.1.4) | protein | 449 | 39% helix, 22% strand | A0A3U8X2F7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- PQ2 · 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13,20,24-hexahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid · ligand · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.80 | 0.83 | 76 | PQ2 |
| 2 | 658 | 0.74 | 0.80 | 66 | SAH, CL |
| 3 | 549 | 0.71 | 0.80 | 62 | CL, SAH |
| 4 | 369 | 0.70 | 0.82 | 43 | CL |
| 5 | 240 | 0.59 | 0.80 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 6456 Ų buried · 80 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VEB · Precorrin-2-bound 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 A0A3U8X2F7
- Elsewhere: RCSB PDB 6VEB · PDBe 6VEB · UniProt A0A3U8X2F7
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