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Crystal structure of ADP-dependent glucokinase from methanocaldococcus jannaschii
Analyse Crystal structure of ADP-dependent glucokinase from methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OD2
- Type
- protein
- Length
- 1,370 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional ADP-specific GLUCOKINASE/PHOSPHOFRUCTOKINASE
- EC
- 2.7.1.146, 2.7.1.147
- UniProt
- Q58999
- Ligands
- 5ID, GLC, MG, PO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bifunctional ADP-specific GLUCOKINASE/PHOSPHOFRUCTOKINASE (EC 2.7.1.146, 2.7.1.147) | protein | 456 | 45% helix, 21% strand | Q58999 |
| B | Bifunctional ADP-specific GLUCOKINASE/PHOSPHOFRUCTOKINASE (EC 2.7.1.146, 2.7.1.147) | protein | 458 | 45% helix, 21% strand | Q58999 |
Ligands and binding sites
- 5ID · (2R,3R,4S,5R)-2-(4-amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3, 4-diol · ligand · 3 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.84 | 0.87 | 92 | GLC, 5ID, MG, PO4 |
| 2 | 954 | 0.84 | 0.85 | 103 | GLC, 5ID, MG, PO4 |
| 3 | 949 | 0.82 | 0.84 | 96 | GLC, 5ID, MG, PO4 |
| 4 | 96 | 0.55 | 0.85 | 18 | empty |
| 5 | 109 | 0.48 | 0.80 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 508 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 287 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5OD2 · Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q58999 · AlphaFold monomer V2.0 prediction for bifunctional ADP-specific… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q58999
- Elsewhere: RCSB PDB 5OD2 · PDBe 5OD2 · UniProt Q58999
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