MolNFT v1 · #4565 · protein
Crystal structure of clavaminate synthase in complex with FE(II), 2- oxoglutarate and N-alpha-L-acetyl arginine
1DRY · Clavaminate synthase 1: “Crystal structure of clavaminate synthase in complex with FE(II), 2- oxoglutarate and N-alpha-L-acetyl…”. X-ray diffraction, 4 ligands (AAG, AKG, FE2), 2 pockets (best druggability 0.73). MolNFT v1 #4565 on…
- PDB
- 1DRY
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clavaminate synthase 1
- UniProt
- Q05581
- Ligands
- AAG, AKG, FE2, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clavaminate synthase 1 | protein | 316 | 29% helix, 22% strand | Q05581 |
Ligands and binding sites
- AAG · N-alpha-L-acetyl-arginine · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.73 | 0.87 | 36 | AAG, FE2, AKG |
| 2 | 62 | 0.33 | 0.76 | 13 | empty |
Compared structures
- 1DRY · Crystal structure of clavaminate synthase in complex with FE(II), 2-oxoglutarate and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05581 · AlphaFold monomer V2.0 prediction for clavaminate synthase 1 (Q05581) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q05581
- Elsewhere: RCSB PDB 1DRY · PDBe 1DRY · UniProt Q05581
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