Research workbench
Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome C551I from paracoccus denitrificans.
Analyse Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GC7
- 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
- P22619, P22364, P29899
- Ligands
- HEC, 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 | — |
| 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 | P29899 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains D, H, L, P
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.82 | 0.93 | 40 | empty |
| 2 | 272 | 0.82 | 0.93 | 39 | empty |
| 3 | 279 | 0.81 | 0.93 | 41 | empty |
| 4 | 274 | 0.81 | 0.93 | 39 | empty |
| 5 | 1175 | 0.80 | 0.81 | 107 | empty |
Interfaces
27 interfaces between chains.
- I–J · 1670 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1662 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1660 Ų buried · 27 hydrogen bonds · protein-protein
- M–N · 1659 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1509 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 8 cofactor, 4 modified (disulfide, heme c attachment, cofactor).
Compared structures
- 2GC7 · Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and… · the same entry in another collection · chain J against J, 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 P22619
- Every structure of UniProt P22364
- Every structure of UniProt P29899
- Elsewhere: RCSB PDB 2GC7 · PDBe 2GC7 · UniProt P22619 · UniProt P22364 · UniProt P29899
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