Research workbench
Crystal structure of the fimx eal domain in complex with reaction product pgpg
Analyse Crystal structure of the fimx eal domain in complex with reaction product pgpg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AFY
- Type
- protein + RNA
- Length
- 503 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimx; 5'-R(*GP*GP)-3'
- EC
- 3.1.4.52
- UniProt
- Q02F59
- Ligands
- MG, NA
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fimx (EC 3.1.4.52) | protein | 249 | 43% helix, 20% strand | Q02F59 |
| B | Fimx (EC 3.1.4.52) | protein | 250 | 44% helix, 20% strand | Q02F59 |
| C, D | 5'-R(*GP*GP)-3' | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, C, B, D
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.79 | 0.81 | 95 | MG |
Interfaces
5 interfaces between chains.
- A–B · 1548 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 511 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 485 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 108 Ų buried · 1 hydrogen bond · protein-nucleic
- B–C · 104 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4AFY · Crystal structure of the FimX EAL domain in complex with reaction product pGpG · 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 Q02F59
- Elsewhere: RCSB PDB 4AFY · PDBe 4AFY · UniProt Q02F59
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