Research workbench
Crystal structure of the quinol form of methylamine dehydrogenase in complex with the diferrous form of maug, C2 space group
Analyse Crystal structure of the quinol form of methylamine dehydrogenase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3I
- Type
- protein
- Length
- 1,713 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylamine utilization protein maug; Methylamine dehydrogenase light chain; Methylamine…
- EC
- 1.-.-.-, 1.4.9.1, 1.4.99.3
- UniProt
- Q51658, P22619, A1BB97
- Ligands
- HEC, NA, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylamine utilization protein maug (EC 1.-.-.-) | protein | 354 | 43% helix, 8% strand | Q51658 |
| B | Methylamine utilization protein maug (EC 1.-.-.-) | protein | 357 | 42% helix, 8% strand | Q51658 |
| C, E | Methylamine dehydrogenase light chain (EC 1.4.9.1) | protein | 125 | 10% helix, 32% strand | P22619 |
| D, F | Methylamine dehydrogenase heavy chain (EC 1.4.99.3) | protein | 376 | 7% helix, 48% strand | A1BB97 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.87 | 0.91 | 95 | CA, HEC |
| 2 | 687 | 0.87 | 0.91 | 93 | HEC |
| 3 | 255 | 0.81 | 0.93 | 37 | empty |
| 4 | 243 | 0.81 | 0.94 | 40 | empty |
| 5 | 959 | 0.78 | 0.80 | 102 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1673 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1672 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 1335 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1303 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 cofactor, 2 modified (disulfide, heme c attachment, nonstandard).
Compared structures
- 4K3I · Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the… · the same entry in another collection · chain F against F, TM-score 1.00
- Q51658 · AlphaFold monomer V2.0 prediction for methylamine utilization protein maug (Q51658) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P22619 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22619) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q51658
- Every structure of UniProt P22619
- Every structure of UniProt A1BB97
- Elsewhere: RCSB PDB 4K3I · PDBe 4K3I · UniProt Q51658 · UniProt P22619 · UniProt A1BB97
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