MolNFT v1 · #163835 · protein
Crystal structure of ancestral flavin-containing monooxygenase (fmo) 2
6SEM: “Crystal structure of ancestral flavin-containing monooxygenase (fmo) 2”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.89). MolNFT v1 #163835 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SEM
- Type
- protein
- Length
- 2,089 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral flavin-containing monooxygenase (fmo) 2
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ancestral flavin-containing monooxygenase (fmo) 2 | protein | 530 | 35% helix, 18% strand | — |
| A | Ancestral flavin-containing monooxygenase (fmo) 2 | protein | 519 | 34% helix, 18% strand | — |
| C, D | Ancestral flavin-containing monooxygenase (fmo) 2 | protein | 520 | 35% helix, 18% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains B, A, C, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.89 | 0.90 | 149 | FAD |
| 2 | 917 | 0.88 | 0.90 | 121 | FAD |
| 3 | 1121 | 0.86 | 0.87 | 103 | FAD |
| 4 | 654 | 0.86 | 0.90 | 81 | FAD |
| 5 | 750 | 0.81 | 0.84 | 88 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2566 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2388 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
- B–A · 78 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SEM · Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 2 · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6SEM · PDBe 6SEM
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