MolNFT v1 · #118994 · protein
Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of paxt-1
5FIR · 5'-3' exoribonuclease 2 homolog: “Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of paxt-1”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.87). MolNFT v1 #118994 on GenesisL1: 3D…
- PDB
- 5FIR
- Type
- protein
- Length
- 4,073 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-3' exoribonuclease 2 homolog; Paxt-1
- EC
- 3.1.13.-
- UniProt
- Q9U299, Q21738
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-3' exoribonuclease 2 homolog (EC 3.1.13.-) | protein | 610 | 48% helix, 12% strand | Q9U299 |
| B | Paxt-1 | protein | 73 | 70% helix, 1% strand | Q21738 |
| C, E | 5'-3' exoribonuclease 2 homolog (EC 3.1.13.-) | protein | 608 | 47% helix, 11% strand | Q9U299 |
| D | Paxt-1 | protein | 71 | 69% helix, 1% strand | Q21738 |
| F | Paxt-1 | protein | 72 | 69% helix, 1% strand | Q21738 |
| G | 5'-3' exoribonuclease 2 homolog (EC 3.1.13.-) | protein | 610 | 47% helix, 12% strand | Q9U299 |
| H, L | Paxt-1 | protein | 69 | 68% helix, 1% strand | Q21738 |
| I | 5'-3' exoribonuclease 2 homolog (EC 3.1.13.-) | protein | 606 | 47% helix, 12% strand | Q9U299 |
| J | Paxt-1 | protein | 67 | 72% helix, 1% strand | Q21738 |
| K | 5'-3' exoribonuclease 2 homolog (EC 3.1.13.-) | protein | 610 | 48% helix, 12% strand | Q9U299 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 27 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.87 | 0.88 | 110 | SO4 |
| 2 | 1086 | 0.87 | 0.88 | 109 | SO4 |
| 3 | 1086 | 0.87 | 0.88 | 98 | SO4 |
| 4 | 990 | 0.86 | 0.88 | 122 | SO4 |
| 5 | 1033 | 0.86 | 0.87 | 106 | SO4 |
Interfaces
17 interfaces between chains.
- E–K · 1455 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 1412 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 1366 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1067 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1064 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 114 modified (engineered).
Compared structures
- 5FIR · Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of PAXT-1 · the same entry in another collection · chain L against L, 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 Q9U299
- Every structure of UniProt Q21738
- Elsewhere: RCSB PDB 5FIR · PDBe 5FIR · UniProt Q9U299 · UniProt Q21738
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