MolNFT v1 · #72596 · protein
Crystal structure of precorrin-4 C11-methyltransferase from rhodobacter capsulatus
3NDC · Precorrin-4 C(11)-methyltransferase: “Crystal structure of precorrin-4 C11-methyltransferase from rhodobacter capsulatus”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.69). MolNFT v1 #72596 on GenesisL1: 3D…
- PDB
- 3NDC
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-4 C(11)-methyltransferase
- EC
- 2.1.1.133
- UniProt
- O68100
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-4 C(11)-methyltransferase (EC 2.1.1.133) | protein | 236 | 34% helix, 23% strand | O68100 |
| B | Precorrin-4 C(11)-methyltransferase (EC 2.1.1.133) | protein | 231 | 30% helix, 23% strand | O68100 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.69 | 0.80 | 55 | SAH |
| 2 | 372 | 0.67 | 0.80 | 45 | SAH |
| 3 | 66 | 0.43 | 0.82 | 19 | empty |
| 4 | 52 | 0.42 | 0.83 | 15 | empty |
| 5 | 54 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2619 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 3NDC · Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus · the same entry in another collection · chain A against A, TM-score 1.00
- O68100 · AlphaFold monomer V2.0 prediction for precorrin-4 C(11)-methyltransferase (O68100) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O68100
- Elsewhere: RCSB PDB 3NDC · PDBe 3NDC · UniProt O68100
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