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Crystal structure of glycerol kinase from elizabethkingia anophelis NUHP1 in complex with ADP and glycerol
Analyse Crystal structure of glycerol kinase from elizabethkingia anophelis NUHP1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UDE
- Type
- protein
- Length
- 1,974 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- A0A077EJ65
- Ligands
- ADP, MG
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase (EC 2.7.1.30) | protein | 493 | 37% helix, 25% strand | A0A077EJ65 |
| B | Glycerol kinase (EC 2.7.1.30) | protein | 495 | 36% helix, 25% strand | A0A077EJ65 |
| C | Glycerol kinase (EC 2.7.1.30) | protein | 494 | 37% helix, 25% strand | A0A077EJ65 |
| D | Glycerol kinase (EC 2.7.1.30) | protein | 492 | 37% helix, 25% strand | A0A077EJ65 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.72 | 0.88 | 38 | empty |
| 2 | 206 | 0.72 | 0.88 | 39 | empty |
| 3 | 330 | 0.69 | 0.83 | 44 | ADP, GOL, MG |
| 4 | 321 | 0.68 | 0.82 | 45 | ADP, GOL, MG |
| 5 | 306 | 0.66 | 0.82 | 46 | ADP, GOL, MG |
Interfaces
4 interfaces between chains.
- A–C · 1868 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1862 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 854 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 766 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6UDE · Crystal structure of Glycerol kinase from Elizabethkingia anophelis NUHP1 in complex with… · the same entry in another collection · chain C against C, 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 A0A077EJ65
- Elsewhere: RCSB PDB 6UDE · PDBe 6UDE · UniProt A0A077EJ65
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