MolNFT v1 · #110177 · protein
F420 complex of coenzyme F420:L-glutamate ligase (fbib) from mycobacterium tuberculosis (C-terminal domain)
4XOQ: “F420 complex of coenzyme F420:L-glutamate ligase (fbib) from mycobacterium tuberculosis (C-terminal domain)”. X-ray diffraction, 2 ligands (F42, SO4), 12 pockets (best druggability 0.79). MolNFT v1 #110177 on GenesisL1: 3D…
- PDB
- 4XOQ
- Type
- protein
- Length
- 803 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
- F42, SO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 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
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