MolNFT v1 · #140954 · protein
Diol dehydratase, ADOCBL/SUBSTRATE-free, anaerobically-prepared crystal
5YRT · Diol dehydrase alpha subunit: “Diol dehydratase, ADOCBL/SUBSTRATE-free, anaerobically-prepared crystal”. X-ray diffraction, 5 ligands (5AD, B12, K), 20 pockets (best druggability 0.86). MolNFT v1 #140954 on GenesisL1: 3D structure…
- PDB
- 5YRT
- Type
- protein
- Length
- 3,474 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diol dehydrase alpha subunit; Diol dehydrase beta subunit; Diol dehydrase gamma subunit
- EC
- 4.2.1.28
- UniProt
- Q59470, Q59471, Q59472
- Ligands
- 5AD, B12, K, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Diol dehydrase alpha subunit (EC 4.2.1.28) | protein | 551 | 51% helix, 10% strand | Q59470 |
| B, K | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 182 | 32% helix, 22% strand | Q59471 |
| C, F, I, L | Diol dehydrase gamma subunit (EC 4.2.1.28) | protein | 136 | 65% helix, 0% strand | Q59472 |
| E | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 178 | 34% helix, 22% strand | Q59471 |
| G, J | Diol dehydrase alpha subunit (EC 4.2.1.28) | protein | 554 | 51% helix, 11% strand | Q59470 |
| H | Diol dehydrase beta subunit (EC 4.2.1.28) | protein | 178 | 32% helix, 22% strand | Q59471 |
Ligands and binding sites
- 5AD · 5'-deoxyadenosine · ligand · 4 copies · chains A, D, G, J
- B12 · Cobalamin · ligand · 4 copies · chains A, B, D, E, G, H, J, K
- K · Potassium ion · metal · 8 copies · chains A, D, G, J
- CA · Calcium ion · metal · 4 copies · chains A, D, G, J
- CL · Chloride ion · ion · 12 copies · chains A, D, C, F, G, J, I, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.86 | 0.87 | 83 | 5AD, B12 |
| 2 | 1133 | 0.86 | 0.87 | 84 | 5AD, B12 |
| 3 | 1159 | 0.86 | 0.87 | 87 | 5AD, B12 |
| 4 | 1187 | 0.85 | 0.86 | 87 | 5AD, B12 |
| 5 | 1196 | 0.74 | 0.77 | 118 | CL |
Interfaces
24 interfaces between chains.
- G–J · 4295 Ų buried · 89 hydrogen bonds · protein-protein
- A–D · 4281 Ų buried · 87 hydrogen bonds · protein-protein
- J–L · 2905 Ų buried · 54 hydrogen bonds · protein-protein
- D–F · 2886 Ų buried · 53 hydrogen bonds · protein-protein
- G–I · 2883 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 5YRT · Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal · 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 Q59470
- Every structure of UniProt Q59471
- Every structure of UniProt Q59472
- Elsewhere: RCSB PDB 5YRT · PDBe 5YRT · UniProt Q59470 · UniProt Q59471 · UniProt Q59472
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