MolNFT v1 · #149147 · protein
Crystal structure of coenzyme F420H2 oxidase (fpra) co-crystallized with 10 mm tb-XO4
6FRM: “Crystal structure of coenzyme F420H2 oxidase (fpra) co-crystallized with 10 mm tb-XO4”. X-ray diffraction, 5 ligands (FMN, 7MT, TB), 20 pockets (best druggability 0.83). MolNFT v1 #149147 on GenesisL1: 3D structure, binding sites…
- PDB
- 6FRM
- Type
- protein
- Length
- 3,222 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420H2 oxidase (fpra)
- Ligands
- FMN, 7MT, TB, FE, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme F420H2 oxidase (fpra) | protein | 402 | 40% helix, 25% strand | — |
| B | Coenzyme F420H2 oxidase (fpra) | protein | 400 | 38% helix, 27% strand | — |
| C, G | Coenzyme F420H2 oxidase (fpra) | protein | 408 | 38% helix, 25% strand | — |
| D | Coenzyme F420H2 oxidase (fpra) | protein | 403 | 39% helix, 25% strand | — |
| E | Coenzyme F420H2 oxidase (fpra) | protein | 397 | 39% helix, 26% strand | — |
| F | Coenzyme F420H2 oxidase (fpra) | protein | 395 | 38% helix, 25% strand | — |
| H | Coenzyme F420H2 oxidase (fpra) | protein | 409 | 39% helix, 25% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- 7MT · Tb-Xo4 · ligand · 2 copies · chains A, D, C, F, G
- TB · Terbium(iii) ion · metal · 14 copies · chains A, B, C, D, E, F, G, H
- FE · Fe (III) ion · metal · 4 copies · chains C, D, G, H
- CL · Chloride ion · ion · 17 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.83 | 0.88 | 57 | FMN |
| 2 | 839 | 0.80 | 0.83 | 64 | TB, FMN |
| 3 | 994 | 0.79 | 0.81 | 124 | empty |
| 4 | 949 | 0.79 | 0.81 | 76 | empty |
| 5 | 907 | 0.79 | 0.81 | 71 | empty |
Interfaces
11 interfaces between chains.
- B–C · 2123 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 2086 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 2065 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 2051 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1644 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6FRM · Crystal Structure of coenzyme F420H2 oxidase (FprA) co-crystallized with 10 mM Tb-Xo4 · 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
- Elsewhere: RCSB PDB 6FRM · PDBe 6FRM
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