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Induced-fit and allosteric effects upon polyene binding revealed by crystal structures of the dynemicin thioesterase
Analyse Induced-fit and allosteric effects upon polyene binding revealed by crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XEM
- Type
- protein
- Length
- 566 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DYNE7
- UniProt
- Q84HI7
- Ligands
- SSV
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DYNE7 | protein | 145 | 25% helix, 44% strand | Q84HI7 |
| B | DYNE7 | protein | 136 | 27% helix, 44% strand | Q84HI7 |
| C | DYNE7 | protein | 139 | 26% helix, 44% strand | Q84HI7 |
| D | DYNE7 | protein | 146 | 23% helix, 43% strand | Q84HI7 |
Ligands and binding sites
- SSV · (3E,5E,7E,9E,11E,13E)-pentadeca-3,5,7,9,11,13-hexaen-2-one · ligand · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.82 | 0.85 | 69 | empty |
| 2 | 304 | 0.77 | 0.88 | 51 | SSV |
| 3 | 146 | 0.68 | 0.88 | 31 | empty |
| 4 | 445 | 0.67 | 0.79 | 61 | empty |
| 5 | 145 | 0.64 | 0.86 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1139 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1001 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 585 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 562 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 436 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XEM · Induced-fit and allosteric effects upon polyene binding revealed by crystal structures of… · 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 Q84HI7
- Elsewhere: RCSB PDB 2XEM · PDBe 2XEM · UniProt Q84HI7
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