Research workbench
Structure of glutamate mutase reconstituted with homo-coenzyme B12
Analyse Structure of glutamate mutase reconstituted with homo-coenzyme B12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H9E
- Type
- protein
- Length
- 1,240 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate mutase sigma subunit; Glutamate mutase epsilon subunit
- EC
- 5.4.99.1
- UniProt
- P80078, P80077
- Ligands
- B12, FWK
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate mutase sigma subunit (EC 5.4.99.1) | protein | 137 | 40% helix, 22% strand | P80078 |
| B, D | Glutamate mutase epsilon subunit (EC 5.4.99.1) | protein | 483 | 52% helix, 9% strand | P80077 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B, C, D
- FWK · (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.86 | 0.87 | 102 | B12, FWK, TAR |
| 2 | 1166 | 0.86 | 0.87 | 97 | B12, FWK, TAR |
| 3 | 100 | 0.46 | 0.80 | 19 | empty |
| 4 | 115 | 0.42 | 0.77 | 22 | empty |
| 5 | 107 | 0.41 | 0.76 | 25 | GOL |
Interfaces
3 interfaces between chains.
- B–D · 1706 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1232 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6H9E · Structure of glutamate mutase reconstituted with homo-coenzyme B12 · the same entry in another collection · chain A against A, TM-score 1.00
- P80077 · AlphaFold monomer V2.0 prediction for glutamate mutase epsilon subunit (P80077) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P80078 · AlphaFold monomer V2.0 prediction for glutamate mutase sigma subunit (P80078) · a predicted model of the same protein · chain A 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 P80078
- Every structure of UniProt P80077
- Elsewhere: RCSB PDB 6H9E · PDBe 6H9E · UniProt P80078 · UniProt P80077
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