Research workbench
Crystal structure of glucdrp from E. COLI K-12 MG1655 (efi target efi- 506058)
Analyse Crystal structure of glucdrp from E. COLI K-12 MG1655 (efi target efi- 506058) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IL0
- Type
- protein
- Length
- 3,442 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase-related protein
- EC
- 4.2.1.-
- UniProt
- Q46915
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glucarate dehydratase-related protein (EC 4.2.1.-) | protein | 440 | 40% helix, 19% strand | Q46915 |
| D | Glucarate dehydratase-related protein (EC 4.2.1.-) | protein | 424 | 38% helix, 19% strand | Q46915 |
| E | Glucarate dehydratase-related protein (EC 4.2.1.-) | protein | 417 | 39% helix, 20% strand | Q46915 |
| F | Glucarate dehydratase-related protein (EC 4.2.1.-) | protein | 439 | 40% helix, 18% strand | Q46915 |
| G | Glucarate dehydratase-related protein (EC 4.2.1.-) | protein | 416 | 39% helix, 20% strand | Q46915 |
| H | Glucarate dehydratase-related protein (EC 4.2.1.-) | protein | 426 | 40% helix, 19% strand | Q46915 |
Ligands and binding sites
- CIT · Citric acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1065 | 0.87 | 0.88 | 139 | empty |
| 2 | 971 | 0.84 | 0.85 | 100 | empty |
| 3 | 634 | 0.84 | 0.88 | 81 | empty |
| 4 | 1159 | 0.83 | 0.84 | 146 | empty |
| 5 | 395 | 0.75 | 0.85 | 51 | CIT |
Interfaces
13 interfaces between chains.
- A–F · 1544 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1521 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1476 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 890 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4IL0 · Crystal structure of GlucDRP from E. coli K-12 MG1655 (EFI target EFI-506058) · the same entry in another collection · chain H against H, TM-score 1.00
- Q46915 · AlphaFold monomer V2.0 prediction for glucarate dehydratase-related protein (Q46915) · a predicted model of the same protein · 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 Q46915
- Elsewhere: RCSB PDB 4IL0 · PDBe 4IL0 · UniProt Q46915
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