MolNFT v1 · #156168 · protein
Structure of dimethylformamidase, dimer
6LVC · N,N-dimethylformamidase large subunit: “Structure of dimethylformamidase, dimer”. Electron microscopy, 1 ligand (FE), 19 pockets (best druggability 0.81). MolNFT v1 #156168 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LVC
- Type
- protein
- Length
- 1,772 residues
- Chains
- 4
- 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
- Ligands
- FE
- Pockets
- 19 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N,N-dimethylformamidase large subunit (EC 3.5.1.56) | protein | 762 | 14% helix, 31% strand | I6NT79 |
| B, D | N,N-dimethylformamidase small subunit (EC 3.5.1.56) | protein | 124 | 48% helix, 14% strand | I6NWZ0 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.81 | 0.83 | 80 | empty |
| 2 | 1044 | 0.79 | 0.80 | 80 | empty |
| 3 | 1097 | 0.78 | 0.80 | 87 | empty |
| 4 | 111 | 0.73 | 0.94 | 30 | empty |
| 5 | 74 | 0.70 | 0.95 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2941 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1998 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1994 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 997 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 997 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6LVC · Structure of Dimethylformamidase, dimer · 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 6LVC · PDBe 6LVC · UniProt I6NT79 · UniProt I6NWZ0
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