MolNFT v1 · #190971 · protein
Amine dehydrogenase MATOUAMDH2 in complex with NADP+
7ZBO: “Amine dehydrogenase MATOUAMDH2 in complex with NADP+”. X-ray diffraction, 1 ligand (NAP), 9 pockets (best druggability 0.84). MolNFT v1 #190971 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ZBO
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine dehydrogenase
- EC
- 1.4.9.98
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amine dehydrogenase (EC 1.4.9.98) | protein | 348 | 33% helix, 27% strand | — |
| B | Amine dehydrogenase (EC 1.4.9.98) | protein | 343 | 31% helix, 27% strand | — |
| C | Amine dehydrogenase (EC 1.4.9.98) | protein | 340 | 32% helix, 28% strand | — |
| D | Amine dehydrogenase (EC 1.4.9.98) | protein | 340 | 32% helix, 28% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.85 | 94 | empty |
| 2 | 577 | 0.71 | 0.80 | 53 | NAP |
| 3 | 576 | 0.70 | 0.79 | 53 | NAP |
| 4 | 318 | 0.69 | 0.83 | 35 | NAP |
| 5 | 151 | 0.57 | 0.82 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1886 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1882 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7ZBO · Amine Dehydrogenase MATOUAmDH2 in complex with NADP+ · 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 7ZBO · PDBe 7ZBO
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