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Co-complex structure of achromobactin synthetase protein D (acsd) with ATP and N-citryl-ethylenediamine from pectobacterium chrysanthemi
Analyse Co-complex structure of achromobactin synthetase protein D (acsd) with ATP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X3J
- Type
- protein
- Length
- 1,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acsd
- UniProt
- Q93AT8
- Ligands
- ATP, X3J, MG
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acsd | protein | 586 | 45% helix, 20% strand | Q93AT8 |
| B | Acsd | protein | 578 | 44% helix, 19% strand | Q93AT8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- X3J · (2S)-2-{2-[(2-aminoethyl)amino]-2-oxoethyl}-2-hydroxybutanedioic acid · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.88 | 0.90 | 132 | ATP, GOL |
| 2 | 581 | 0.86 | 0.91 | 80 | ATP, MG, GOL, X3J |
| 3 | 57 | 0.39 | 0.81 | 14 | GOL |
| 4 | 59 | 0.35 | 0.78 | 15 | empty |
| 5 | 60 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 942 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2X3J · Co-complex structure of achromobactin synthetase protein D (acsd) with ATP and… · 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 2X3J · PDBe 2X3J · UniProt Q93AT8
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