Research workbench
Amine dehydrogenase from petrotoga mobilis; open and closed form
Analyse Amine dehydrogenase from petrotoga mobilis; open and closed form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G1M
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase
- UniProt
- A9BHL2
- Ligands
- NAD, PO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dihydrodipicolinate reductase | protein | 334 | 33% helix, 28% strand | A9BHL2 |
| B | Dihydrodipicolinate reductase | protein | 332 | 33% helix, 28% strand | A9BHL2 |
| C | Dihydrodipicolinate reductase | protein | 335 | 33% helix, 28% strand | A9BHL2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.75 | 0.87 | 43 | NAD |
| 2 | 278 | 0.72 | 0.86 | 44 | NAD |
| 3 | 395 | 0.61 | 0.76 | 34 | NAD, PO4 |
| 4 | 374 | 0.60 | 0.77 | 40 | NAD, PO4 |
| 5 | 151 | 0.44 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1846 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1809 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6G1M · Amine Dehydrogenase from Petrotoga mobilis; open and closed form · 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 A9BHL2
- Elsewhere: RCSB PDB 6G1M · PDBe 6G1M · UniProt A9BHL2
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