Research workbench
Crystal structure of protein L-isoaspartyl methyltransferase from escherichia COLI
Analyse Crystal structure of protein L-isoaspartyl methyltransferase from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LBF
- Type
- protein
- Length
- 817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-L-isoaspartate O-methyltransferase
- EC
- 2.1.1.77
- UniProt
- P0A7A5
- Ligands
- SAH, PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 207 | 35% helix, 27% strand | P0A7A5 |
| D | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 196 | 33% helix, 28% strand | P0A7A5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.76 | 0.80 | 122 | GOL, SAH |
| 2 | 163 | 0.70 | 0.89 | 38 | SAH |
| 3 | 200 | 0.70 | 0.87 | 42 | SAH |
| 4 | 616 | 0.66 | 0.76 | 56 | empty |
| 5 | 205 | 0.66 | 0.84 | 41 | SAH |
Interfaces
5 interfaces between chains.
- A–B · 645 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 602 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 256 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LBF · Crystal structure of Protein L-isoaspartyl methyltransferase from Escherichia coli · the same entry in another collection · chain D against D, TM-score 1.00
- P0A7A5 · AlphaFold monomer V2.0 prediction for protein-L-isoaspartate O-methyltransferase (P0A7A5) · a predicted model of the same protein · chain C 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 P0A7A5
- Elsewhere: RCSB PDB 3LBF · PDBe 3LBF · UniProt P0A7A5
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