Research workbench
Crystal structure of bacillus subtilis bacc dihydroanticapsin 7- dehydrogenase
Analyse Crystal structure of bacillus subtilis bacc dihydroanticapsin 7- dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ITW
- Type
- protein
- Length
- 1,020 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroanticapsin 7-dehydrogenase
- EC
- 1.1.1.385
- UniProt
- P39640
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydroanticapsin 7-dehydrogenase (EC 1.1.1.385) | protein | 255 | 53% helix, 16% strand | P39640 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.86 | 0.88 | 60 | empty |
| 2 | 658 | 0.76 | 0.81 | 69 | empty |
| 3 | 635 | 0.75 | 0.81 | 60 | SO4 |
| 4 | 576 | 0.75 | 0.82 | 47 | SO4 |
| 5 | 537 | 0.74 | 0.82 | 47 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 1623 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1616 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1563 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1561 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ITW · Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase · the same entry in another collection · chain D against D, TM-score 1.00
- P39640 · AlphaFold monomer V2.0 prediction for dihydroanticapsin 7-dehydrogenase (P39640) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P39640
- Elsewhere: RCSB PDB 5ITW · PDBe 5ITW · UniProt P39640
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