Research workbench
Crystal structure of the W199E-MAUG/PRE-methylamine dehydrogenase complex
Analyse Crystal structure of the W199E-MAUG/PRE-methylamine dehydrogenase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RN1
- Type
- protein
- Length
- 1,716 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.-.-.-, 1.4.99.3
- UniProt
- Q51658, A1BBA0, A1BB97
- Ligands
- HEC, NA, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylamine utilization protein maug (EC 1.-.-.-) | protein | 354 | 42% helix, 8% strand | Q51658 |
| B | Methylamine utilization protein maug (EC 1.-.-.-) | protein | 355 | 42% helix, 8% strand | Q51658 |
| C | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 131 | 10% helix, 32% strand | A1BBA0 |
| D, F | Methylamine dehydrogenase heavy chain (EC 1.4.99.3) | protein | 376 | 7% helix, 47% strand | A1BB97 |
| E | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 124 | 10% helix, 34% strand | A1BBA0 |
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 · chains B
- 1PE · Pentaethylene glycol · additive · chains F
- PG4 · Tetraethylene glycol · additive · chains F
- ACT · Acetate ion · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.87 | 0.91 | 94 | CA, HEC |
| 2 | 683 | 0.87 | 0.91 | 91 | HEC |
| 3 | 245 | 0.81 | 0.93 | 41 | empty |
| 4 | 240 | 0.81 | 0.93 | 42 | empty |
| 5 | 989 | 0.78 | 0.80 | 107 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1702 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1671 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1335 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 1314 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 cofactor, 2 modified (disulfide, heme c attachment, nonstandard).
Compared structures
- 3RN1 · Crystal Structure of the W199E-MauG/pre-Methylamine Dehydrogenase Complex · 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 B against A, 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 Q51658
- Every structure of UniProt A1BBA0
- Every structure of UniProt A1BB97
- Elsewhere: RCSB PDB 3RN1 · PDBe 3RN1 · UniProt Q51658 · UniProt A1BBA0 · UniProt A1BB97
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