Research workbench
Crystal structure of daca from staphylococcus aureus in complex with apcpp
Analyse Crystal structure of daca from staphylococcus aureus in complex with apcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GYX
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diadenylate cyclase
- EC
- 2.7.7.85
- UniProt
- A0A2P7CAT2
- Ligands
- APC, MN
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Diadenylate cyclase (EC 2.7.7.85) | protein | 152 | 38% helix, 24% strand | A0A2P7CAT2 |
| A | Diadenylate cyclase (EC 2.7.7.85) | protein | 149 | 39% helix, 24% strand | A0A2P7CAT2 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains B, A
- MN · Manganese (II) ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.32 | 0.76 | 11 | APC |
Interfaces
1 interface between chains.
- B–A · 743 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6GYX · Crystal structure of DacA from Staphylococcus aureus in complex with ApCpp · 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 A0A2P7CAT2
- Elsewhere: RCSB PDB 6GYX · PDBe 6GYX · UniProt A0A2P7CAT2
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