Research workbench
Cryo-EM structure of dfga-B at 2.54 ångström resolution
Analyse Cryo-EM structure of dfga-B at 2.54 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DRE
- Type
- protein
- Length
- 1,572 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar phosphate ISOMERASE/EPIMERASE; Dfgb
- UniProt
- I5AX50, I5AX49
- Pockets
- 14 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Sugar phosphate ISOMERASE/EPIMERASE | protein | 276 | 44% helix, 19% strand | I5AX50 |
| B, D, F, H | Dfgb | protein | 117 | 9% helix, 53% strand | I5AX49 |
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.85 | 0.90 | 81 | empty |
| 2 | 807 | 0.85 | 0.88 | 90 | empty |
| 3 | 658 | 0.72 | 0.79 | 75 | empty |
| 4 | 603 | 0.72 | 0.80 | 65 | empty |
| 5 | 271 | 0.67 | 0.83 | 33 | empty |
Interfaces
20 interfaces between chains.
- A–D · 842 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 842 Ų buried · 5 hydrogen bonds · protein-protein
- E–H · 829 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 829 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 780 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7DRE · Cryo-EM structure of DfgA-B at 2.54 angstrom resolution · the same entry in another collection · chain A against A, 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 I5AX50
- Every structure of UniProt I5AX49
- Elsewhere: RCSB PDB 7DRE · PDBe 7DRE · UniProt I5AX50 · UniProt I5AX49
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