MolNFT v1 · #40833 · protein
X-ray reduced paraccocus denitrificans methylamine dehydrogenase N-quinol in complex with amicyanin.
2J57: “X-ray reduced paraccocus denitrificans methylamine dehydrogenase N-quinol in complex with amicyanin.”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.81). MolNFT v1 #40833 on GenesisL1: 3D structure, binding sites…
- PDB
- 2J57
- Type
- protein
- Length
- 2,448 residues
- Chains
- 12
- 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Amicyanin | protein | 105 | 3% helix, 50% strand | P22364 |
| G, H, I, J | Methylamine dehydrogenase heavy chain (EC 1.4.99.3) | protein | 382 | 8% helix, 47% strand | P29894 |
| K, L, M, N | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 125 | 10% helix, 28% strand | P22619 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.81 | 0.94 | 37 | empty |
| 2 | 237 | 0.81 | 0.94 | 38 | empty |
| 3 | 247 | 0.81 | 0.93 | 41 | empty |
| 4 | 258 | 0.81 | 0.93 | 37 | empty |
| 5 | 1070 | 0.80 | 0.82 | 109 | empty |
Interfaces
22 interfaces between chains.
- H–L · 1680 Ų buried · 31 hydrogen bonds · protein-protein
- G–N · 1667 Ų buried · 30 hydrogen bonds · protein-protein
- I–K · 1659 Ų buried · 26 hydrogen bonds · protein-protein
- J–M · 1652 Ų buried · 28 hydrogen bonds · protein-protein
- I–N · 1475 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 4 modified (disulfide, nonstandard).
Compared structures
- 2J57 · X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex… · the same entry in another collection · chain N against N, 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 P22364
- Every structure of UniProt P29894
- Every structure of UniProt P22619
- Elsewhere: RCSB PDB 2J57 · PDBe 2J57 · UniProt P22364 · UniProt P29894 · UniProt P22619
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