Research workbench
Crystal structure of bacillus subtilis bacc dihydroanticapsin 7- dehydrogenase in complex with NADH
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
- 5ITV
- Type
- protein
- Length
- 992 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
- NAI
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dihydroanticapsin 7-dehydrogenase (EC 1.1.1.385) | protein | 255 | 52% helix, 16% strand | P39640 |
| D | Dihydroanticapsin 7-dehydrogenase (EC 1.1.1.385) | protein | 227 | 49% helix, 18% strand | P39640 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.85 | 0.87 | 61 | empty |
| 2 | 657 | 0.75 | 0.81 | 54 | NAI |
| 3 | 608 | 0.75 | 0.81 | 47 | NAI |
| 4 | 577 | 0.74 | 0.81 | 48 | NAI |
| 5 | 281 | 0.57 | 0.77 | 34 | NAI |
Interfaces
6 interfaces between chains.
- A–B · 1704 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1586 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1580 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1568 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 227 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ITV · Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase in complex… · the same entry in another collection · chain C against C, TM-score 1.00
- P39640 · AlphaFold monomer V2.0 prediction for dihydroanticapsin 7-dehydrogenase (P39640) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 5ITV · PDBe 5ITV · UniProt P39640
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