MolNFT v1 · #152430 · protein
Crystal structure of a standalone versatile eal protein from vibrio cholerae O395 - 3',3'-cgamp bound form
6IH7 · Cyclic di nucleotide phoshodiesterase: “Crystal structure of a standalone versatile eal protein from vibrio cholerae O395 - 3',3'-cgamp bound form”. X-ray diffraction, 2 ligands (4BW, CA), 4 pockets (best druggability 0.58). MolNFT…
- PDB
- 6IH7
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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 B against B, 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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