Research workbench
NMR structure of glutamate mutase (B12-binding subunit) complexed with the vitamin B12 nucleotide
Analyse NMR structure of glutamate mutase (B12-binding subunit) complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ID8
- Type
- protein
- Length
- 137 residues
- Chains
- 1
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylaspartate mutase S chain
- EC
- 5.4.99.1
- UniProt
- Q05488
- Ligands
- FOP, DBI
- Pockets
- 3 · best druggability 0.75
Structure
solution nmr · 1 distinct chain · 23% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylaspartate mutase S chain (EC 5.4.99.1) | protein | 137 | 23% helix, 17% strand | Q05488 |
Ligands and binding sites
- FOP · 2-hydroxy-propyl-ammonium · ligand · chains A
- DBI · Phosphoric acid mono-[5-(5,6-dimethyl-benzoimidazol-1-yl)-4-hydroxy-2-hydroxymethyl-tetrahydro-furan-3-yl] ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.75 | 0.98 | 19 | empty |
| 2 | 183 | 0.55 | 0.80 | 24 | DBI |
| 3 | 54 | 0.29 | 0.75 | 13 | empty |
Compared structures
- 1ID8 · NMR structure of glutamate mutase (B12-binding subunit) complexed with the vitamin B12… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05488 · AlphaFold monomer V2.0 prediction for glutamate mutase sigma subunit (Q05488) · a predicted model of the same protein · chain A against A, TM-score 0.68
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 Q05488
- Elsewhere: RCSB PDB 1ID8 · PDBe 1ID8 · UniProt Q05488
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