Research workbench
Structure of amine dehydrogenase from mycobacterium smegmatis
Analyse Structure of amine dehydrogenase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IAQ
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase N-terminus domain-containing protein
- EC
- 1.17.1.8
- UniProt
- A0A0D6I8P6
- Ligands
- NAP
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate reductase N-terminus domain-containing protein (EC 1.17.1.8) | protein | 338 | 35% helix, 27% strand | A0A0D6I8P6 |
| B | Dihydrodipicolinate reductase N-terminus domain-containing protein (EC 1.17.1.8) | protein | 336 | 36% helix, 27% strand | A0A0D6I8P6 |
| C | Dihydrodipicolinate reductase N-terminus domain-containing protein (EC 1.17.1.8) | protein | 335 | 36% helix, 27% strand | A0A0D6I8P6 |
| D | Dihydrodipicolinate reductase N-terminus domain-containing protein (EC 1.17.1.8) | protein | 339 | 35% helix, 27% strand | A0A0D6I8P6 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.73 | 0.84 | 41 | EDO, NAP |
| 2 | 314 | 0.72 | 0.84 | 37 | EDO, NAP |
| 3 | 296 | 0.71 | 0.84 | 39 | EDO, NAP |
| 4 | 295 | 0.69 | 0.83 | 40 | EDO, NAP |
| 5 | 71 | 0.50 | 0.85 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1753 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1731 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 147 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IAQ · Structure of Amine Dehydrogenase from Mycobacterium smegmatis · 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 A0A0D6I8P6
- Elsewhere: RCSB PDB 6IAQ · PDBe 6IAQ · UniProt A0A0D6I8P6
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