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Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 3',3'-cGAMP bound form
Analyse Crystal structure of a standalone versatile EAL protein from Vibrio cholerae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IH7
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
- Molecule
- cyclic di nucleotide phoshodiesterase
- EC
- 3.1.4.52
- UniProt
- A0A0H3AJ04
- Ligands
- 4BW, CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · resolution 2.25 · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | cyclic di nucleotide phoshodiesterase (EC 3.1.4.52) | protein | 237 | 38% helix, 22% strand | A0A0H3AJ04 |
Ligands and binding sites
- 4BW · 2-amino-9-[(2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9, 2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one · ligand · 2 copies · chains B, A
- CA · Calcium ion · metal · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.58 | 0.77 | 40 | 4BW |
| 2 | 288 | 0.57 | 0.77 | 43 | 4BW |
| 3 | 134 | 0.50 | 0.79 | 22 | empty |
| 4 | 70 | 0.38 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 999 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6IH7 · Crystal structure of a standalone versatile eal protein from vibrio cholerae O395… · 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 A0A0H3AJ04
- Elsewhere: RCSB PDB 6IH7 · PDBe 6IH7 · UniProt A0A0H3AJ04
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