MolNFT v1 · #172068 · protein
Crystal structure of chaetomium thermophilum glycerol kinase in complex with substrate in P1 space group
6ZQ4 · Glycerol kinase-like protein: “Crystal structure of chaetomium thermophilum glycerol kinase in complex with substrate in P1 space group”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.80). MolNFT v1 #172068 on…
- PDB
- 6ZQ4
- Type
- protein
- Length
- 4,084 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase-like protein
- UniProt
- G0SAG9
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase-like protein | protein | 510 | 37% helix, 22% strand | G0SAG9 |
| B | Glycerol kinase-like protein | protein | 510 | 37% helix, 22% strand | G0SAG9 |
| C | Glycerol kinase-like protein | protein | 509 | 37% helix, 22% strand | G0SAG9 |
| D | Glycerol kinase-like protein | protein | 509 | 37% helix, 22% strand | G0SAG9 |
| E, H | Glycerol kinase-like protein | protein | 511 | 37% helix, 21% strand | G0SAG9 |
| F, G | Glycerol kinase-like protein | protein | 512 | 37% helix, 22% strand | G0SAG9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.80 | 0.81 | 77 | empty |
| 2 | 1043 | 0.79 | 0.80 | 93 | PO4, GOL |
| 3 | 1051 | 0.78 | 0.80 | 110 | GOL |
| 4 | 754 | 0.73 | 0.79 | 92 | empty |
| 5 | 555 | 0.71 | 0.80 | 57 | PO4, GOL |
Interfaces
12 interfaces between chains.
- B–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 402 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 386 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 358 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 347 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZQ4 · Crystal structure of Chaetomium thermophilum Glycerol Kinase in complex with substrate in… · the same entry in another collection · chain H against H, 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 G0SAG9
- Elsewhere: RCSB PDB 6ZQ4 · PDBe 6ZQ4 · UniProt G0SAG9
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