MolNFT v1 · #139649 · protein
Crystal structure of methanol dehydrogenase from methylophaga aminisulfidivorans
5XM3 · Glucose dehydrogenase: “Crystal structure of methanol dehydrogenase from methylophaga aminisulfidivorans”. X-ray diffraction, 2 ligands (PQQ, MG), 9 pockets (best druggability 0.78). MolNFT v1 #139649 on GenesisL1: 3D structure…
- PDB
- 5XM3
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose dehydrogenase; Methanol dehydrogenase [cytochrome C] subunit 2
- EC
- 1.1.2.7
- UniProt
- A3FJ48, A3FJ51
- Ligands
- PQQ, MG
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glucose dehydrogenase | protein | 596 | 12% helix, 35% strand | A3FJ48 |
| B, D | Methanol dehydrogenase [cytochrome C] subunit 2 (EC 1.1.2.7) | protein | 66 | 41% helix, 3% strand | A3FJ51 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 28 | PQQ, MG |
| 2 | 98 | 0.77 | 0.98 | 30 | PQQ, MG |
| 3 | 406 | 0.59 | 0.76 | 66 | empty |
| 4 | 67 | 0.47 | 0.83 | 15 | empty |
| 5 | 70 | 0.45 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2152 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2113 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2097 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5XM3 · Crystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans · the same entry in another collection · chain A 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 A3FJ48
- Every structure of UniProt A3FJ51
- Elsewhere: RCSB PDB 5XM3 · PDBe 5XM3 · UniProt A3FJ48 · UniProt A3FJ51
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