MolNFT v1 · #14562 · protein
Crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin
1MDA · Methylamine dehydrogenase (heavy subunit): “Crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.81). MolNFT v1 #14562…
- PDB
- 1MDA
- Type
- protein
- Length
- 1,184 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylamine dehydrogenase (heavy subunit); Methylamine dehydrogenase (light subunit)…
- EC
- 1.4.99.3
- UniProt
- P22364
- Ligands
- CU
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Methylamine dehydrogenase (heavy subunit) (EC 1.4.99.3) | protein | 368 | 3% helix, 42% strand | — |
| L, M | Methylamine dehydrogenase (light subunit) (EC 1.4.99.3) | protein | 121 | 6% helix, 29% strand | — |
| A, B | Amicyanin | protein | 103 | 0% helix, 33% strand | P22364 |
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
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.81 | 0.94 | 39 | empty |
| 2 | 245 | 0.81 | 0.94 | 40 | empty |
| 3 | 1125 | 0.78 | 0.80 | 114 | empty |
| 4 | 54 | 0.67 | 0.96 | 20 | empty |
| 5 | 109 | 0.66 | 0.90 | 23 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1425 Ų buried · 10 hydrogen bonds · protein-protein
- J–M · 1400 Ų buried · 13 hydrogen bonds · protein-protein
- L–J · 1302 Ų buried · 20 hydrogen bonds · protein-protein
- H–M · 1301 Ų buried · 22 hydrogen bonds · protein-protein
- H–J · 574 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 modified (disulfide, cofactor).
Compared structures
- 1MDA · Crystal structure of an electron-transfer complex between methylamine dehydrogenase and… · the same entry in another collection · chain B against B, TM-score 1.00
- P22364 · AlphaFold monomer V2.0 prediction for amicyanin (P22364) · a predicted model of the same protein · chain B against A, TM-score 0.94
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
- Elsewhere: RCSB PDB 1MDA · PDBe 1MDA · UniProt P22364
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