Research workbench
Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome C551I from paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 a resolution.
Analyse Structural comparison of the oxidized ternary electron transfer complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GC4
- 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; Amicyanin…
- EC
- 1.4.99.3
- UniProt
- P29894, P22619, P22364, P29899
- Ligands
- HEC, CU, NA
- 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 | 42% helix, 1% strand | P29899 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.82 | 0.93 | 40 | empty |
| 2 | 272 | 0.82 | 0.93 | 39 | empty |
| 3 | 264 | 0.81 | 0.93 | 37 | empty |
| 4 | 271 | 0.81 | 0.93 | 37 | empty |
| 5 | 1184 | 0.79 | 0.81 | 114 | empty |
Interfaces
27 interfaces between chains.
- I–J · 1676 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1669 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1661 Ų buried · 28 hydrogen bonds · protein-protein
- M–N · 1649 Ų buried · 25 hydrogen bonds · protein-protein
- I–N · 1504 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 8 cofactor, 4 modified (disulfide, heme c attachment, cofactor).
Compared structures
- 2GC4 · Structural comparison of the oxidized ternary electron transfer complex of methylamine… · 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 P29899
- Elsewhere: RCSB PDB 2GC4 · PDBe 2GC4 · UniProt P29894 · UniProt P22619 · UniProt P22364 · UniProt P29899
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