Research workbench
Structure of dimethylformamidase, tetramer
Analyse Structure of dimethylformamidase, tetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LVB
- Type
- protein
- Length
- 3,544 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
- Ligands
- FE
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | N,N-dimethylformamidase large subunit (EC 3.5.1.56) | protein | 762 | 14% helix, 31% strand | I6NT79 |
| B, D, F, H | 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 · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 854 | 0.81 | 0.83 | 79 | empty |
| 2 | 886 | 0.81 | 0.83 | 80 | empty |
| 3 | 975 | 0.81 | 0.82 | 130 | empty |
| 4 | 1091 | 0.78 | 0.80 | 88 | empty |
| 5 | 1053 | 0.78 | 0.80 | 84 | empty |
Interfaces
14 interfaces between chains.
- E–G · 2950 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2945 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1969 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1969 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1967 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6LVB · Structure of Dimethylformamidase, tetramer · 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 6LVB · PDBe 6LVB · UniProt I6NT79 · UniProt I6NWZ0
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