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Co-complex structure of achromobactin synthetase protein D ( acsd) with AMP and sulfate from pectobacterium chrysanthemi
Analyse Co-complex structure of achromobactin synthetase protein D ( acsd) with AMP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X3K
- Type
- protein
- Length
- 1,145 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acsd
- UniProt
- Q93AT8
- Ligands
- AMP, SO4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acsd | protein | 575 | 43% helix, 20% strand | Q93AT8 |
| B | Acsd | protein | 570 | 44% helix, 20% strand | Q93AT8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.85 | 0.89 | 86 | AMP, SO4 |
| 2 | 681 | 0.84 | 0.88 | 78 | AMP, SO4 |
| 3 | 292 | 0.71 | 0.85 | 49 | empty |
| 4 | 104 | 0.65 | 0.89 | 24 | empty |
| 5 | 87 | 0.34 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 847 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2X3K · Co-complex structure of achromobactin synthetase protein D (acsd) with AMP and sulfate… · 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 Q93AT8
- Elsewhere: RCSB PDB 2X3K · PDBe 2X3K · UniProt Q93AT8
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