MolNFT v1 · #156169 · protein
Structure of dimethylformamidase, tetramer, Y440A mutant
6LVD · N,N-dimethylformamidase large subunit: “Structure of dimethylformamidase, tetramer, Y440A mutant”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #156169 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LVD
- Type
- protein
- Length
- 3,464 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N,N-dimethylformamidase large subunit; N,N-dimethylformamidase small subunit
- EC
- 3.5.1.56
- UniProt
- I6NT79, I6NWZ0
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 18% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | N,N-dimethylformamidase large subunit (EC 3.5.1.56) | protein | 747 | 13% helix, 31% strand | I6NT79 |
| B, D, F, H | N,N-dimethylformamidase small subunit (EC 3.5.1.56) | protein | 119 | 53% helix, 6% strand | I6NWZ0 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.85 | 0.86 | 87 | empty |
| 2 | 1146 | 0.83 | 0.84 | 96 | empty |
| 3 | 1165 | 0.83 | 0.84 | 92 | empty |
| 4 | 1178 | 0.82 | 0.83 | 86 | empty |
| 5 | 807 | 0.81 | 0.84 | 76 | empty |
Interfaces
14 interfaces between chains.
- A–C · 2685 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 2682 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1495 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1469 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1455 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LVD · Structure of Dimethylformamidase, tetramer, Y440A mutant · 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 I6NT79
- Every structure of UniProt I6NWZ0
- Elsewhere: RCSB PDB 6LVD · PDBe 6LVD · UniProt I6NT79 · UniProt I6NWZ0
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