Research workbench
FMN complex of coenzyme F420:L-glutamate ligase (fbib) from mycobacterium tuberculosis (C-terminal domain)
Analyse FMN 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
- 4XOO
- Type
- protein
- Length
- 784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420:L-glutamate ligase
- EC
- 6.3.2.31, 6.3.2.34
- UniProt
- P9WP79
- Ligands
- FMN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 196 | 48% helix, 18% strand | P9WP79 |
| B | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 201 | 51% helix, 17% strand | P9WP79 |
| C | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 199 | 50% helix, 15% strand | P9WP79 |
| D | Coenzyme F420:L-glutamate ligase (EC 6.3.2.31, 6.3.2.34) | protein | 188 | 51% helix, 19% strand | P9WP79 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.76 | 0.78 | 115 | FMN |
| 2 | 771 | 0.73 | 0.79 | 79 | FMN |
| 3 | 544 | 0.73 | 0.81 | 54 | FMN |
| 4 | 469 | 0.71 | 0.81 | 39 | FMN |
| 5 | 144 | 0.45 | 0.77 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2956 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2954 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 204 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XOO · FMN 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 A against A, TM-score 0.99
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 4XOO · PDBe 4XOO · UniProt P9WP79
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