Research workbench
Coenzyme F420:L-glutamate ligase (fbib) from mycobacterium tuberculosis (C-terminal domain).
Analyse Coenzyme F420:L-glutamate ligase (fbib) from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XOM
- Type
- protein
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420:L-glutamate ligase
- UniProt
- P9WP79
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme F420:L-glutamate ligase | protein | 206 | 50% helix, 15% strand | P9WP79 |
| B | Coenzyme F420:L-glutamate ligase | protein | 205 | 51% helix, 15% strand | P9WP79 |
| C | Coenzyme F420:L-glutamate ligase | protein | 193 | 48% helix, 16% strand | P9WP79 |
| D | Coenzyme F420:L-glutamate ligase | protein | 178 | 48% helix, 17% strand | P9WP79 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.79 | 0.81 | 91 | empty |
| 2 | 303 | 0.69 | 0.83 | 38 | empty |
| 3 | 522 | 0.69 | 0.79 | 56 | empty |
| 4 | 357 | 0.67 | 0.80 | 34 | empty |
| 5 | 213 | 0.47 | 0.75 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3364 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2589 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 491 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 195 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XOM · Coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium tuberculosis (C-terminal… · 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 4XOM · PDBe 4XOM · UniProt P9WP79
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