MolNFT v1 · #72585 · protein
Crystal structure of precorrin-6A synthase from rhodobacter capsulatus
3ND1 · Precorrin-6A SYNTHASE/COBF protein: “Crystal structure of precorrin-6A synthase from rhodobacter capsulatus”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability 0.76). MolNFT v1 #72585 on GenesisL1: 3D structure…
- PDB
- 3ND1
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-6A SYNTHASE/COBF protein
- EC
- 2.1.1.-
- UniProt
- O68102
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-6A SYNTHASE/COBF protein (EC 2.1.1.-) | protein | 244 | 37% helix, 26% strand | O68102 |
| B | Precorrin-6A SYNTHASE/COBF protein (EC 2.1.1.-) | protein | 249 | 37% helix, 25% strand | O68102 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.76 | 0.82 | 65 | SAH |
| 2 | 668 | 0.76 | 0.82 | 60 | SAH |
| 3 | 107 | 0.37 | 0.75 | 24 | ACT |
| 4 | 88 | 0.34 | 0.74 | 23 | ACT |
Interfaces
1 interface between chains.
- A–B · 1829 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 3ND1 · Crystal structure of Precorrin-6A synthase from Rhodobacter capsulatus · the same entry in another collection · chain B against B, 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 O68102
- Elsewhere: RCSB PDB 3ND1 · PDBe 3ND1 · UniProt O68102
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