Research workbench
Crystal structure of the quinoprotein methylamine dehydrogenase from paracoccus denitrificans at 1.75 ångströms
Analyse Crystal structure of the quinoprotein methylamine dehydrogenase from paracoccus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BBK
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylamine dehydrogenase (heavy subunit); Methylamine dehydrogenase (light subunit)
- EC
- 1.4.99.3
- UniProt
- P29894, P22619
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Methylamine dehydrogenase (heavy subunit) (EC 1.4.99.3) | protein | 355 | 3% helix, 50% strand | P29894 |
| L, M | Methylamine dehydrogenase (light subunit) (EC 1.4.99.3) | protein | 125 | 10% helix, 33% strand | P22619 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.81 | 0.93 | 43 | empty |
| 2 | 267 | 0.81 | 0.93 | 40 | empty |
| 3 | 970 | 0.78 | 0.80 | 102 | empty |
| 4 | 64 | 0.43 | 0.82 | 25 | empty |
| 5 | 60 | 0.39 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- J–M · 1623 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 1620 Ų buried · 28 hydrogen bonds · protein-protein
- L–J · 1045 Ų buried · 22 hydrogen bonds · protein-protein
- H–M · 1037 Ų buried · 20 hydrogen bonds · protein-protein
- H–J · 711 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 modified (disulfide, cofactor).
Compared structures
- 2BBK · Crystal structure of the quinoprotein methylamine dehydrogenase from paracoccus… · the same entry in another collection · chain M against M, TM-score 1.00
- P29894 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase heavy chain (P29894) · a predicted model of the same protein · chain H against A, TM-score 1.00
- P22619 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22619) · a predicted model of the same protein · chain L against A, TM-score 0.99
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 P29894
- Every structure of UniProt P22619
- Elsewhere: RCSB PDB 2BBK · PDBe 2BBK · UniProt P29894 · UniProt P22619
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