Research workbench
Glycerol dehydratase-cyanocobalamin complex of klebsiella pneumoniae
Analyse Glycerol dehydratase-cyanocobalamin complex of klebsiella pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IWP
- Type
- protein
- Length
- 1,754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol dehydratase alpha subunit; Glycerol dehydratase beta subunit; Glycerol…
- EC
- 4.2.1.30
- UniProt
- Q59476, O08505, Q59475
- Ligands
- B12, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Glycerol dehydratase alpha subunit (EC 4.2.1.30) | protein | 555 | 51% helix, 10% strand | Q59476 |
| B, E | Glycerol dehydratase beta subunit (EC 4.2.1.30) | protein | 184 | 33% helix, 24% strand | O08505 |
| G, M | Glycerol dehydratase gamma subunit (EC 4.2.1.30) | protein | 138 | 62% helix, 1% 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
- 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 | 1165 | 0.85 | 0.86 | 87 | PGO, B12 |
| 2 | 1198 | 0.85 | 0.86 | 83 | PGO, B12 |
| 3 | 149 | 0.63 | 0.85 | 36 | empty |
| 4 | 160 | 0.61 | 0.84 | 37 | empty |
| 5 | 295 | 0.56 | 0.76 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–L · 4145 Ų buried · 73 hydrogen bonds · protein-protein
- A–G · 2742 Ų buried · 52 hydrogen bonds · protein-protein
- L–M · 2736 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 22 hydrogen bonds · protein-protein
- L–E · 1636 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1IWP · Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae · 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 1IWP · PDBe 1IWP · UniProt Q59476 · UniProt O08505 · UniProt Q59475
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