MolNFT v1 · #14649 · protein
Mutation of alpha PHE55 of methylamine dehydrogenase alters the reorganization energy and electronic coupling for its electron transfer reaction with amicyanin
1MG2 · Methylamine dehydrogenase, heavy chain: “Mutation of alpha PHE55 of methylamine dehydrogenase alters the reorganization energy and electronic coupling…”. X-ray diffraction, 4 ligands (HEC, CU, NA), 20 pockets (best druggability…
- PDB
- 1MG2
- Type
- protein
- Length
- 3,036 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylamine dehydrogenase, heavy chain; Methylamine dehydrogenase, light chain…
- EC
- 1.4.99.3
- UniProt
- P29894, P22619, P22364, P29889
- Ligands
- HEC, CU, NA, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Methylamine dehydrogenase, heavy chain (EC 1.4.99.3) | protein | 382 | 8% helix, 47% strand | P29894 |
| B, F, J, N | Methylamine dehydrogenase, light chain (EC 1.4.99.3) | protein | 125 | 10% helix, 30% strand | P22619 |
| C, G, K, O | Amicyanin | protein | 105 | 3% helix, 50% strand | P22364 |
| D, H, L, P | Cytochrome C-L | protein | 147 | 43% helix, 1% strand | P29889 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains D, H, L, P
- CU · Copper (II) ion · metal · 4 copies · chains C, G, K, O
- NA · Sodium ion · metal · 4 copies · chains C, D, G, H, K, L, O, P
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, E, F, G, I, J, K, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 262 | 0.82 | 0.94 | 42 | PO4 |
| 2 | 266 | 0.81 | 0.93 | 39 | PO4 |
| 3 | 255 | 0.81 | 0.93 | 37 | PO4 |
| 4 | 255 | 0.80 | 0.93 | 39 | PO4 |
| 5 | 561 | 0.78 | 0.85 | 83 | empty |
Interfaces
27 interfaces between chains.
- E–F · 1611 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1609 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 1603 Ų buried · 27 hydrogen bonds · protein-protein
- M–N · 1601 Ų buried · 27 hydrogen bonds · protein-protein
- J–M · 1520 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 8 cofactor, 4 modified (disulfide, heme c attachment, cofactor).
Compared structures
- 1MG2 · Mutation of alpha PHE55 of methylamine dehydrogenase alters the reorganization energy and… · the same entry in another collection · chain K against K, 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 P29894
- Every structure of UniProt P22619
- Every structure of UniProt P22364
- Every structure of UniProt P29889
- Elsewhere: RCSB PDB 1MG2 · PDBe 1MG2 · UniProt P29894 · UniProt P22619 · UniProt P22364 · UniProt P29889
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