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Crystal structure of the thioesterase domain of deoxyerythronolide B synthase in complex with a small phosphonate inhibitor
Analyse Crystal structure of the thioesterase domain of deoxyerythronolide B synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D3Z
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythronolide synthase, modules 5 and 6
- EC
- 2.3.1.94
- UniProt
- Q03133
- Ligands
- 57H, CA
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythronolide synthase, modules 5 and 6 (EC 2.3.1.94) | protein | 263 | 42% helix, 15% strand | Q03133 |
Ligands and binding sites
- 57H · prop-2-en-1-ylphosphonic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.80 | 0.89 | 44 | 57H, 1PE |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5D3Z · Crystal structure of the thioesterase domain of deoxyerythronolide B synthase in complex… · 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 Q03133
- Elsewhere: RCSB PDB 5D3Z · PDBe 5D3Z · UniProt Q03133
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