Research workbench
Crystal Structure Analysis of the Glycotransferase of kitacinnamycin
Analyse Crystal Structure Analysis of the Glycotransferase of kitacinnamycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J31
- Type
- protein
- Length
- 1,582 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.244
- Source
- Kitasatospora; SYNTHETIC CONSTRUCT
- Molecule
- kcn28; Dbb-dsg-val-mea-val-gly-gly-dva-dle
- Ligands
- BG9
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.244 · 4 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | kcn28 | protein | 385 | 45% helix, 15% strand | — |
| B | kcn28 | protein | 387 | 45% helix, 15% strand | — |
| C, D | kcn28 | protein | 387 | 45% helix, 15% strand | — |
| E, F, G, H | Dbb-dsg-val-mea-val-gly-gly-dva-dle | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- BG9 · (2E,2'E)-3,3'-(1,2-phenylene)di(prop-2-enoic acid) · ligand · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.82 | 0.83 | 105 | BG9 |
| 2 | 1043 | 0.82 | 0.83 | 95 | BG9 |
| 3 | 1145 | 0.81 | 0.82 | 98 | BG9 |
| 4 | 1144 | 0.77 | 0.79 | 95 | BG9 |
| 5 | 243 | 0.61 | 0.81 | 52 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1204 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 746 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 729 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 720 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 719 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 d-amino, 8 modified, 4 covalent (D-amino acid, nonstandard, covalent ligand).
Compared structures
- 6J31 · Crystal structure analysis of the glycotransferase of kitacinnamycin · 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
- Elsewhere: RCSB PDB 6J31 · PDBe 6J31
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