Research workbench
Structure of Dimethylformamidase, tetramer, E521A mutant
Analyse Structure of Dimethylformamidase, tetramer, E521A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LVE
- Type
- protein
- Length
- 3,480 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Paracoccus sp. SSG05
- Molecule
- N,N-dimethylformamidase large subunit; N,N-dimethylformamidase small subunit
- EC
- 3.5.1.56
- UniProt
- I6NT79, I6NWZ0
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.1 · 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 | 751 | 13% helix, 32% strand | I6NT79 |
| B, D, F, H | N,N-dimethylformamidase small subunit (EC 3.5.1.56) | protein | 119 | 50% helix, 8% 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 | 819 | 0.81 | 0.84 | 77 | empty |
| 2 | 780 | 0.81 | 0.84 | 56 | empty |
| 3 | 1096 | 0.81 | 0.82 | 79 | empty |
| 4 | 836 | 0.81 | 0.83 | 71 | empty |
| 5 | 1107 | 0.80 | 0.82 | 88 | empty |
Interfaces
14 interfaces between chains.
- E–G · 2693 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2690 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1560 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1554 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1547 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6LVE · Structure of dimethylformamidase, tetramer, E521A 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 6LVE · PDBe 6LVE · UniProt I6NT79 · UniProt I6NWZ0
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