Research workbench
F420 complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium tuberculosis (C-terminal domain)
Analyse F420 complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XOQ
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- Coenzyme F420:L-glutamate ligase
- EC
- 6.3.2.31, 6.3.2.34
- UniProt
- P9WP79
- Ligands
- F42, SO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.05 · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 204 | 50% helix, 15% strand | P9WP79 |
| C | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 197 | 48% helix, 15% strand | P9WP79 |
| D | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 198 | 50% helix, 15% strand | P9WP79 |
Ligands and binding sites
- F42 · Coenzyme F420 · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.79 | 0.81 | 101 | F42 |
| 2 | 613 | 0.70 | 0.78 | 71 | empty |
| 3 | 514 | 0.69 | 0.79 | 58 | F42 |
| 4 | 325 | 0.67 | 0.81 | 39 | F42 |
| 5 | 135 | 0.47 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3322 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2973 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 497 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XOQ · F420 complex of coenzyme F420:L-glutamate ligase (fbib) from mycobacterium tuberculosis… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WP79 · AlphaFold monomer V2.0 prediction for bifunctional F420 biosynthesis protein fbib (P9WP79) · a predicted model of the same protein · chain B 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 P9WP79
- Elsewhere: RCSB PDB 4XOQ · PDBe 4XOQ · UniProt P9WP79
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.