Research workbench
Crystal structure of a standalone versatile eal protein from vibrio cholerae O395 - apo 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
- 6IFQ
- 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
- CA
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Cyclic di nucleotide phoshodiesterase (EC 3.1.4.52) | protein | 237 | 41% helix, 21% strand | A0A0H3AJ04 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.70 | 0.95 | 16 | empty |
| 2 | 362 | 0.59 | 0.76 | 39 | empty |
| 3 | 325 | 0.57 | 0.76 | 38 | empty |
| 4 | 86 | 0.44 | 0.80 | 18 | empty |
| 5 | 53 | 0.40 | 0.81 | 11 | empty |
Interfaces
1 interface between chains.
- B–A · 1107 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6IFQ · Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - Apo… · 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 6IFQ · PDBe 6IFQ · UniProt A0A0H3AJ04
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