MolNFT v1 · #166017 · protein
Crystal structure of glycerol kinase from elizabethkingia anophelis NUHP1 in complex with ADP and glycerol
6UDE: “Crystal structure of glycerol kinase from elizabethkingia anophelis NUHP1 in complex with ADP and glycerol”. X-ray diffraction, 2 ligands (ADP, MG), 19 pockets (best druggability 0.72). MolNFT v1 #166017 on GenesisL1: 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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