Research workbench
Structure of B. megaterium NFRA2
Analyse Structure of B. megaterium NFRA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HEI
- Type
- protein
- Length
- 1,967 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NFRA2
- UniProt
- A0A0K0VJM8
- Ligands
- FMN, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | NFRA2 | protein | 246 | 50% helix, 14% strand | A0A0K0VJM8 |
| C | NFRA2 | protein | 245 | 50% helix, 14% strand | A0A0K0VJM8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 5 copies · chains C, D, H, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.76 | 0.81 | 54 | empty |
| 2 | 502 | 0.73 | 0.82 | 61 | FMN |
| 3 | 967 | 0.73 | 0.77 | 61 | SO4 |
| 4 | 551 | 0.72 | 0.81 | 60 | FMN |
| 5 | 445 | 0.70 | 0.81 | 48 | FMN |
Interfaces
15 interfaces between chains.
- C–D · 5365 Ų buried · 88 hydrogen bonds · protein-protein
- E–F · 5347 Ų buried · 93 hydrogen bonds · protein-protein
- A–B · 5345 Ų buried · 81 hydrogen bonds · protein-protein
- G–H · 5325 Ų buried · 87 hydrogen bonds · protein-protein
- B–F · 971 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5HEI · Structure of B. megaterium NfrA2 · the same entry in another collection · chain D against D, 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 A0A0K0VJM8
- Elsewhere: RCSB PDB 5HEI · PDBe 5HEI · UniProt A0A0K0VJM8
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