Research workbench
Glycerol dehydratase reactivase
Analyse Glycerol dehydratase reactivase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NBW
- Type
- protein
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol dehydratase reactivase alpha subunit; Glycerol dehydratase reactivase beta…
- UniProt
- Q59474, Q48423
- Ligands
- CA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol dehydratase reactivase alpha subunit | protein | 606 | 33% helix, 31% strand | Q59474 |
| B, D | Glycerol dehydratase reactivase beta subunit | protein | 113 | 35% helix, 22% strand | Q48423 |
| C | Glycerol dehydratase reactivase alpha subunit | protein | 604 | 33% helix, 30% strand | Q59474 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.83 | 0.84 | 115 | empty |
| 2 | 944 | 0.77 | 0.80 | 103 | empty |
| 3 | 762 | 0.77 | 0.81 | 118 | empty |
| 4 | 331 | 0.64 | 0.80 | 41 | empty |
| 5 | 280 | 0.53 | 0.75 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2117 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 804 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 799 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 388 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 384 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1NBW · Glycerol dehydratase reactivase · 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 Q59474
- Every structure of UniProt Q48423
- Elsewhere: RCSB PDB 1NBW · PDBe 1NBW · UniProt Q59474 · UniProt Q48423
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