Research workbench
Crystal structure of escherichia COLI flavin trafficking protein, an FMN transferase
Analyse Crystal structure of escherichia COLI flavin trafficking protein, an FMN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XGV
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD:PROTEIN FMN transferase
- EC
- 2.7.1.180
- UniProt
- P0AB85
- Ligands
- CA, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 309 | 37% helix, 26% strand | P0AB85 |
| B | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 309 | 36% helix, 28% strand | P0AB85 |
| C | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 309 | 34% helix, 26% strand | P0AB85 |
| D | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 305 | 36% helix, 27% strand | P0AB85 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, D, C
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.82 | 0.83 | 82 | EDO |
| 2 | 1170 | 0.82 | 0.83 | 83 | EDO |
| 3 | 543 | 0.71 | 0.80 | 50 | EDO |
| 4 | 639 | 0.70 | 0.78 | 51 | EDO |
| 5 | 436 | 0.64 | 0.78 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1625 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1602 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 372 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 188 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XGV · Crystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase · the same entry in another collection · chain C against C, TM-score 1.00
- P0AB85 · AlphaFold monomer V2.0 prediction for FAD:PROTEIN FMN transferase (P0AB85) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P0AB85
- Elsewhere: RCSB PDB 4XGV · PDBe 4XGV · UniProt P0AB85
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