Research workbench
Crystal structure of the diol dehydratase-adeninylpentylcobalamin complex from klebsiella oxytoca
Analyse Crystal structure of the diol dehydratase-adeninylpentylcobalamin complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EEX
- Type
- protein
- Length
- 1,732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propanediol dehydratase
- EC
- 4.2.1.28
- UniProt
- Q59470, Q59471, Q59472
- Ligands
- COY, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Propanediol dehydratase (EC 4.2.1.28) | protein | 551 | 51% helix, 10% strand | Q59470 |
| B, E | Propanediol dehydratase (EC 4.2.1.28) | protein | 178 | 34% helix, 22% strand | Q59471 |
| G, M | Propanediol dehydratase (EC 4.2.1.28) | protein | 137 | 63% helix, 1% strand | Q59472 |
Ligands and binding sites
- COY · Co-(adenin-9-yl-pentyl)-cobalamin · ligand · 2 copies · chains A, B, L, E
- K · Potassium ion · metal · 4 copies · chains A, L
- PGO · S-1,2-propanediol · additive · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.85 | 0.87 | 76 | COY, PGO |
| 2 | 1177 | 0.84 | 0.85 | 82 | COY, PGO |
| 3 | 128 | 0.70 | 0.91 | 28 | empty |
| 4 | 125 | 0.69 | 0.91 | 28 | empty |
| 5 | 144 | 0.63 | 0.85 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–L · 4314 Ų buried · 86 hydrogen bonds · protein-protein
- A–G · 2756 Ų buried · 52 hydrogen bonds · protein-protein
- L–M · 2736 Ų buried · 41 hydrogen bonds · protein-protein
- L–E · 1451 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1EEX · Crystal structure of the diol dehydratase-adeninylpentylcobalamin complex from klebsiella… · 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 1EEX · PDBe 1EEX · UniProt Q59470 · UniProt Q59471 · UniProt Q59472
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