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Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-GMP 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
- 6IH1
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- 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
- C2E, CA
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.95 · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | cyclic di nucleotide phoshodiesterase (EC 3.1.4.52) | protein | 237 | 36% helix, 21% strand | A0A0H3AJ04 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.71 | 0.83 | 54 | empty |
| 2 | 63 | 0.67 | 0.95 | 16 | empty |
| 3 | 508 | 0.65 | 0.77 | 57 | C2E, CA |
| 4 | 428 | 0.62 | 0.76 | 55 | C2E, CA |
| 5 | 484 | 0.62 | 0.75 | 60 | C2E |
Interfaces
5 interfaces between chains.
- A–C · 1093 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1080 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 153 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 151 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6IH1 · 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 6IH1 · PDBe 6IH1 · UniProt A0A0H3AJ04
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