MolNFT v1 · #97094 · protein
Crystal structure of the quinol form of methylamine dehydrogenase in complex with the diferrous form of maug, C2 space group
4K3I · Methylamine utilization protein maug: “Crystal structure of the quinol form of methylamine dehydrogenase in complex with the diferrous form of maug…”. X-ray diffraction, 3 ligands (HEC, NA, CA), 20 pockets (best druggability 0.87).…
- 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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