MolNFT v1 · #59740 · protein
Paracoccus versutus methylamine dehydrogenase in complex with amicyanin
3C75 · Methylamine dehydrogenase heavy chain: “Paracoccus versutus methylamine dehydrogenase in complex with amicyanin”. X-ray diffraction, 1 ligand (CU), 11 pockets (best druggability 0.81). MolNFT v1 #59740 on GenesisL1: 3D structure…
- PDB
- 3C75
- Type
- protein
- Length
- 1,212 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylamine dehydrogenase heavy chain; Methylamine dehydrogenase light chain; Amicyanin
- EC
- 1.4.99.3
- UniProt
- P23006, P22641, P22365
- Ligands
- CU
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Methylamine dehydrogenase heavy chain (EC 1.4.99.3) | protein | 375 | 6% helix, 47% strand | P23006 |
| L, M | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 125 | 10% helix, 29% strand | P22641 |
| A, B | Amicyanin | protein | 106 | 3% helix, 45% strand | P22365 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.81 | 0.82 | 113 | empty |
| 2 | 101 | 0.77 | 0.98 | 31 | empty |
| 3 | 98 | 0.75 | 0.96 | 33 | empty |
| 4 | 465 | 0.69 | 0.80 | 55 | empty |
| 5 | 428 | 0.67 | 0.79 | 52 | empty |
Interfaces
9 interfaces between chains.
- J–M · 1641 Ų buried · 26 hydrogen bonds · protein-protein
- H–L · 1640 Ų buried · 28 hydrogen bonds · protein-protein
- L–J · 1396 Ų buried · 17 hydrogen bonds · protein-protein
- H–M · 1386 Ų buried · 18 hydrogen bonds · protein-protein
- H–J · 700 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 modified (disulfide, cofactor).
Compared structures
- 3C75 · Paracoccus versutus methylamine dehydrogenase in complex with amicyanin · the same entry in another collection · chain B against B, TM-score 1.00
- P22641 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22641) · a predicted model of the same protein · chain M against A, TM-score 0.99
- P22365 · AlphaFold monomer V2.0 prediction for amicyanin (P22365) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P23006 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase heavy chain (P23006) · a predicted model of the same protein · chain J against A, TM-score 0.97
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 P23006
- Every structure of UniProt P22641
- Every structure of UniProt P22365
- Elsewhere: RCSB PDB 3C75 · PDBe 3C75 · UniProt P23006 · UniProt P22641 · UniProt P22365
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