Research workbench
Crystal structure of yeco from haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine
Analyse Crystal structure of yeco from haemophilus influenzae (HI0319), a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IM8
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeco
- EC
- 2.1.1.-
- UniProt
- P43985
- Ligands
- SAI, CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yeco (EC 2.1.1.-) | protein | 225 | 48% helix, 21% strand | P43985 |
| B | Yeco (EC 2.1.1.-) | protein | 223 | 49% helix, 24% strand | P43985 |
Ligands and binding sites
- SAI · S-adenosyl-L-homoselenocysteine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.75 | 0.82 | 62 | CL, SAI |
| 2 | 227 | 0.68 | 0.85 | 43 | CL, SAI |
| 3 | 104 | 0.52 | 0.82 | 23 | empty |
| 4 | 63 | 0.31 | 0.75 | 14 | empty |
| 5 | 61 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 499 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1IM8 · Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with… · the same entry in another collection · chain A against A, TM-score 1.00
- P43985 · AlphaFold monomer V2.0 prediction for carboxy-S-adenosyl-L-methionine synthase (P43985) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P43985
- Elsewhere: RCSB PDB 1IM8 · PDBe 1IM8 · UniProt P43985
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