Research workbench
Crystal structure of precorrin-4 C11-methyltransferase from rhodobacter capsulatus (no sah bound)
Analyse Crystal structure of precorrin-4 C11-methyltransferase from rhodobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NEI
- Type
- protein
- Length
- 449 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
- SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-4 C(11)-methyltransferase (EC 2.1.1.133) | protein | 225 | 33% helix, 25% strand | O68100 |
| B | Precorrin-4 C(11)-methyltransferase (EC 2.1.1.133) | protein | 224 | 33% helix, 25% strand | O68100 |
Ligands and binding sites
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 | 347 | 0.70 | 0.83 | 41 | SO4 |
| 2 | 410 | 0.65 | 0.79 | 41 | SO4 |
| 3 | 56 | 0.34 | 0.78 | 15 | empty |
| 4 | 67 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2238 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 3NEI · Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus (no… · 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 0.96
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 3NEI · PDBe 3NEI · UniProt O68100
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