Research workbench
X-ray reduced paraccocus denitrificans methylamine dehydrogenase N-semiquinone in complex with amicyanin.
Analyse X-ray reduced paraccocus denitrificans methylamine dehydrogenase N-semiquinone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J56
- Type
- protein
- Length
- 1,209 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amicyanin; Methylamine dehydrogenase heavy chain; Methylamine dehydrogenase light chain
- EC
- 1.4.99.3
- UniProt
- P22364, P29894, P22619
- Ligands
- CU, NA
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amicyanin | protein | 105 | 3% helix, 50% strand | P22364 |
| H, J | Methylamine dehydrogenase heavy chain (EC 1.4.99.3) | protein | 375 | 7% helix, 48% strand | P29894 |
| L | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 125 | 10% helix, 30% strand | P22619 |
| M | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 124 | 10% helix, 29% strand | P22619 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains H, L, J, M
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.81 | 0.93 | 38 | empty |
| 2 | 261 | 0.81 | 0.93 | 43 | empty |
| 3 | 1007 | 0.78 | 0.80 | 106 | empty |
| 4 | 286 | 0.61 | 0.79 | 42 | empty |
| 5 | 202 | 0.57 | 0.79 | 29 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1672 Ų buried · 26 hydrogen bonds · protein-protein
- J–M · 1656 Ų buried · 31 hydrogen bonds · protein-protein
- H–M · 1420 Ų buried · 20 hydrogen bonds · protein-protein
- J–L · 1392 Ų buried · 18 hydrogen bonds · protein-protein
- H–J · 710 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 2J56 · X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiqui in complex… · 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 J against A, TM-score 1.00
- P22364 · AlphaFold monomer V2.0 prediction for amicyanin (P22364) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P22619 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22619) · a predicted model of the same protein · chain M 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 P22364
- Every structure of UniProt P29894
- Every structure of UniProt P22619
- Elsewhere: RCSB PDB 2J56 · PDBe 2J56 · UniProt P22364 · UniProt P29894 · UniProt P22619
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