Research workbench
Mutation of alpha PHE55 of methylamine dehydrogenase alters the reorganization energy and electronic coupling for its electron transfer reaction with amicyanin
Analyse Mutation of alpha PHE55 of methylamine dehydrogenase alters the reorganization… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MG3
- 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, 48% strand | P29894 |
| B, F, J, N | Methylamine dehydrogenase, light chain (EC 1.4.99.3) | protein | 125 | 10% helix, 32% strand | P22619 |
| C, G, K, O | Amicyanin | protein | 105 | 3% helix, 49% strand | P22364 |
| D, H, L, P | Cytochrome C-L | protein | 147 | 41% 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 | 279 | 0.82 | 0.93 | 39 | PO4 |
| 2 | 275 | 0.81 | 0.93 | 39 | PO4 |
| 3 | 270 | 0.81 | 0.93 | 39 | PO4 |
| 4 | 858 | 0.81 | 0.84 | 111 | empty |
| 5 | 281 | 0.81 | 0.92 | 43 | PO4 |
Interfaces
26 interfaces between chains.
- E–F · 1615 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1610 Ų buried · 29 hydrogen bonds · protein-protein
- M–N · 1604 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1604 Ų buried · 33 hydrogen bonds · protein-protein
- I–N · 1510 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 8 disulfide, 4 modified (heme c attachment, disulfide, nonstandard).
Compared structures
- 1MG3 · 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 1MG3 · PDBe 1MG3 · UniProt P29894 · UniProt P22619 · UniProt P22364 · UniProt P29889
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