Research workbench
Tmm in complex with methimazole
Analyse Tmm in complex with methimazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GSN
- Type
- protein
- Length
- 1,780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.203
- Source
- Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)
- Molecule
- Flavin-containing monooxygenase
- UniProt
- A3SLM3
- Ligands
- NAP, FAD, MMZ
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.203 · 1 distinct chain · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Flavin-containing monooxygenase | protein | 445 | 31% helix, 21% strand | A3SLM3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- MMZ · 1-methyl-1,3-dihydro-2H-imidazole-2-thione · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.85 | 0.86 | 113 | NAP, FAD |
| 2 | 844 | 0.85 | 0.87 | 99 | NAP, FAD |
| 3 | 1053 | 0.83 | 0.84 | 109 | NAP, FAD, MMZ |
| 4 | 1066 | 0.83 | 0.84 | 106 | NAP, FAD, MMZ |
| 5 | 742 | 0.72 | 0.78 | 102 | empty |
Interfaces
5 interfaces between chains.
- A–D · 433 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 404 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 211 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 146 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GSN · Tmm in complex with methimazole · 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 A3SLM3
- Elsewhere: RCSB PDB 5GSN · PDBe 5GSN · UniProt A3SLM3
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