MolNFT v1 · #14845 · protein
Crystal structure of substrate free form of glycerol dehydratase
1MMF · Glycerol dehydrase alpha subunit: “Crystal structure of substrate free form of glycerol dehydratase”. X-ray diffraction, 2 ligands (B12, K), 20 pockets (best druggability 0.85). MolNFT v1 #14845 on GenesisL1: 3D structure, binding…
- PDB
- 1MMF
- Type
- protein
- Length
- 1,735 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol dehydrase alpha subunit; Glycerol dehydrase beta subunit; Glycerol dehydrase…
- EC
- 4.2.1.30
- UniProt
- Q59476, O08505, Q59475
- Ligands
- B12, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol dehydrase alpha subunit (EC 4.2.1.30) | protein | 552 | 51% helix, 11% strand | Q59476 |
| B | Glycerol dehydrase beta subunit (EC 4.2.1.30) | protein | 181 | 33% helix, 20% strand | O08505 |
| G | Glycerol dehydrase gamma subunit (EC 4.2.1.30) | protein | 132 | 56% helix, 2% strand | Q59475 |
| L | Glycerol dehydrase alpha subunit (EC 4.2.1.30) | protein | 555 | 50% helix, 10% strand | Q59476 |
| E | Glycerol dehydrase beta subunit (EC 4.2.1.30) | protein | 184 | 32% helix, 24% strand | O08505 |
| M | Glycerol dehydrase gamma subunit (EC 4.2.1.30) | protein | 131 | 56% helix, 2% strand | Q59475 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B, L, E
- K · Potassium ion · metal · 2 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.85 | 0.86 | 84 | B12 |
| 2 | 1195 | 0.85 | 0.86 | 83 | B12 |
| 3 | 124 | 0.69 | 0.91 | 31 | empty |
| 4 | 244 | 0.66 | 0.83 | 38 | empty |
| 5 | 320 | 0.57 | 0.76 | 35 | empty |
Interfaces
9 interfaces between chains.
- A–L · 4258 Ų buried · 70 hydrogen bonds · protein-protein
- A–G · 2752 Ų buried · 43 hydrogen bonds · protein-protein
- L–M · 2722 Ų buried · 42 hydrogen bonds · protein-protein
- L–E · 1607 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1MMF · Crystal structure of substrate free form of glycerol dehydratase · the same entry in another collection · chain A against A, TM-score 1.00
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 Q59476
- Every structure of UniProt O08505
- Every structure of UniProt Q59475
- Elsewhere: RCSB PDB 1MMF · PDBe 1MMF · UniProt Q59476 · UniProt O08505 · UniProt Q59475
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