Research workbench
Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide B synthase
Analyse Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QO3
- Type
- protein
- Length
- 1,742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eryaii erythromycin polyketide synthase modules 3 and 4
- EC
- 2.3.1.94
- UniProt
- A4F7P0
- Ligands
- CER, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eryaii erythromycin polyketide synthase modules 3 and 4 (EC 2.3.1.94) | protein | 869 | 38% helix, 18% strand | A4F7P0 |
| B | Eryaii erythromycin polyketide synthase modules 3 and 4 (EC 2.3.1.94) | protein | 873 | 38% helix, 18% strand | A4F7P0 |
Ligands and binding sites
- CER · (2S, 3R)-3-hydroxy-4-oxo-7,10-trans,trans-dodecadienamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.87 | 0.88 | 119 | CER |
| 2 | 289 | 0.66 | 0.82 | 36 | ACT |
| 3 | 329 | 0.66 | 0.81 | 41 | ACT |
| 4 | 349 | 0.59 | 0.77 | 51 | empty |
| 5 | 318 | 0.57 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 2199 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2QO3 · Crystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase · 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 A4F7P0
- Elsewhere: RCSB PDB 2QO3 · PDBe 2QO3 · UniProt A4F7P0
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