Research workbench
Crystal structure of a glucosylglycerol phosphorylase from Marinobacter adhaerens
Analyse Crystal structure of a glucosylglycerol phosphorylase from Marinobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XDR
- Type
- protein
- Length
- 8,638 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Marinobacter adhaerens
- Molecule
- Glucosylglycerol phosphorylase
- EC
- 2.4.1.359
- UniProt
- E4PMA5
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, H, I, J, K, L, M, N, O, P, Q, R | Glucosylglycerol phosphorylase (EC 2.4.1.359) | protein | 480 | 40% helix, 21% strand | E4PMA5 |
| E, G | Glucosylglycerol phosphorylase (EC 2.4.1.359) | protein | 479 | 39% helix, 20% strand | E4PMA5 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.83 | 0.84 | 109 | empty |
| 2 | 802 | 0.79 | 0.83 | 91 | empty |
| 3 | 822 | 0.79 | 0.82 | 82 | empty |
| 4 | 784 | 0.79 | 0.83 | 110 | empty |
| 5 | 700 | 0.78 | 0.82 | 102 | empty |
Interfaces
42 interfaces between chains.
- A–B · 1203 Ų buried · 18 hydrogen bonds · protein-protein
- C–R · 1192 Ų buried · 22 hydrogen bonds · protein-protein
- D–G · 1173 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 771 Ų buried · 12 hydrogen bonds · protein-protein
- F–J · 751 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- E4PMA5 · AlphaFold monomer V2.0 prediction for glucosylglycerol phosphorylase (E4PMA5) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 E4PMA5
- Elsewhere: RCSB PDB 7XDR · PDBe 7XDR · UniProt E4PMA5
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