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Crystal structure of the N-terminal N-formyltransferase domain (residues 1-306) of escherichia COLI arna in complex with udp-ARA4N and folinic acid
Analyse Crystal structure of the N-terminal N-formyltransferase domain (residues 1-306)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J63
- Type
- protein
- Length
- 1,189 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional polymyxin resistance protein arna
- UniProt
- F4SGI5
- Ligands
- G3N, FNX
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional polymyxin resistance protein arna | protein | 302 | 29% helix, 28% strand | F4SGI5 |
| B | Bifunctional polymyxin resistance protein arna | protein | 301 | 30% helix, 27% strand | F4SGI5 |
| C | Bifunctional polymyxin resistance protein arna | protein | 285 | 32% helix, 27% strand | F4SGI5 |
| D | Bifunctional polymyxin resistance protein arna | protein | 301 | 31% helix, 30% strand | F4SGI5 |
Ligands and binding sites
- G3N · (2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- FNX · (4aS,6S)-2-amino-6-{(E)-[(4-methylphenyl)imino]methyl}-4-oxo-4,6,7,8-tetrahydropteridine-5(4aH)-carbaldehyde · ligand · 4 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.83 | 0.88 | 67 | G3N, FNX |
| 2 | 483 | 0.81 | 0.88 | 54 | G3N, FNX |
| 3 | 834 | 0.80 | 0.83 | 94 | G3N, FNX |
| 4 | 890 | 0.79 | 0.81 | 91 | G3N, FNX |
| 5 | 705 | 0.64 | 0.74 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1274 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 885 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 819 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 624 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5J63 · Crystal Structure of the N-terminal N-formyltransferase Domain (residues 1-306) of… · the same entry in another collection · chain A 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 F4SGI5
- Elsewhere: RCSB PDB 5J63 · PDBe 5J63 · UniProt F4SGI5
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