MolNFT v1 · #150966 · protein
Structure of glutamate mutase reconstituted with bishomo-coenzyme B12
6H9F · Glutamate mutase sigma subunit: “Structure of glutamate mutase reconstituted with bishomo-coenzyme B12”. X-ray diffraction, 2 ligands (B12, 8ZB), 13 pockets (best druggability 0.86). MolNFT v1 #150966 on GenesisL1: 3D structure…
- PDB
- 6H9F
- 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, 8ZB
- Pockets
- 13 · 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 | 53% helix, 9% strand | P80077 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B, C, D
- 8ZB · (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol · ligand · 2 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
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.86 | 0.87 | 99 | B12, 8ZB, TAR |
| 2 | 1169 | 0.85 | 0.86 | 100 | B12, 8ZB, TAR |
| 3 | 177 | 0.49 | 0.77 | 23 | empty |
| 4 | 102 | 0.46 | 0.79 | 23 | empty |
| 5 | 99 | 0.45 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1699 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1192 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6H9F · Structure of glutamate mutase reconstituted with bishomo-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 D 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 6H9F · PDBe 6H9F · UniProt P80078 · UniProt P80077
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