Research workbench
Crystal structure of a ternary electron transfer complex between methylamine dehydrogenase, amicyanin and a C-type cytochrome
Analyse Crystal structure of a ternary electron transfer complex between methylamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2MTA
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- 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
- P29894, P22619, P22364, P29899
- Ligands
- HEC, CU, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Methylamine dehydrogenase (heavy subunit) (EC 1.4.99.3) | protein | 373 | 6% helix, 47% strand | P29894 |
| L | Methylamine dehydrogenase (light subunit) (EC 1.4.99.3) | protein | 125 | 10% helix, 34% strand | P22619 |
| A | Amicyanin | protein | 105 | 3% helix, 50% strand | P22364 |
| C | Cytochrome C551I | protein | 147 | 42% helix, 1% strand | P29899 |
Ligands and binding sites
- HEC · Heme C · ligand · chains C
- CU · Copper (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.81 | 0.93 | 42 | empty |
| 2 | 458 | 0.71 | 0.81 | 49 | HEC |
| 3 | 361 | 0.63 | 0.78 | 39 | empty |
| 4 | 234 | 0.60 | 0.80 | 27 | empty |
| 5 | 417 | 0.55 | 0.73 | 50 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1677 Ų buried · 29 hydrogen bonds · protein-protein
- L–A · 502 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 433 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 317 Ų buried · 4 hydrogen bonds · protein-protein
- H–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 cofactor, 1 modified (disulfide, heme c attachment, cofactor).
Compared structures
- 2MTA · Crystal structure of a ternary electron transfer complex between methylamine… · the same entry in another collection · chain C against C, TM-score 1.00
- P29894 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase heavy chain (P29894) · a predicted model of the same protein · chain H against A, TM-score 0.99
- P22619 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22619) · a predicted model of the same protein · chain L against A, TM-score 0.99
- P22364 · AlphaFold monomer V2.0 prediction for amicyanin (P22364) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P29899 · AlphaFold monomer V2.0 prediction for cytochrome C-L (P29899) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P29899
- Elsewhere: RCSB PDB 2MTA · PDBe 2MTA · UniProt P29894 · UniProt P22619 · UniProt P22364 · UniProt P29899
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