MolNFT v1 · #110277 · protein
Structure of the PNKP1/RNL/HEN1 RNA repair complex
4XRP: “Structure of the PNKP1/RNL/HEN1 RNA repair complex”. X-ray diffraction, 3 ligands (MG, SO4, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #110277 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XRP
- Type
- protein
- Length
- 2,255 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PNKP1; Rnl; HEN1
- UniProt
- C2M8N3, C2M8N4, C2M7I7
- Ligands
- MG, SO4, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | PNKP1 | protein | 311 | 38% helix, 19% strand | C2M8N3 |
| B | Rnl | protein | 394 | 47% helix, 16% strand | C2M8N4 |
| C | HEN1 | protein | 424 | 37% helix, 22% strand | C2M7I7 |
| E | Rnl | protein | 393 | 47% helix, 17% strand | C2M8N4 |
| F | HEN1 | protein | 422 | 36% helix, 23% strand | C2M7I7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 5 copies · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.79 | 0.81 | 81 | MG |
| 2 | 1065 | 0.79 | 0.81 | 97 | MG |
| 3 | 701 | 0.78 | 0.82 | 62 | SO4 |
| 4 | 723 | 0.76 | 0.81 | 76 | MG, GOL |
| 5 | 199 | 0.74 | 0.90 | 38 | empty |
Interfaces
10 interfaces between chains.
- A–D · 3657 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1744 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1733 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 621 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4XRP · Structure of the Pnkp1/Rnl/Hen1 RNA repair complex · the same entry in another collection · chain B against B, 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 C2M8N3
- Every structure of UniProt C2M8N4
- Every structure of UniProt C2M7I7
- Elsewhere: RCSB PDB 4XRP · PDBe 4XRP · UniProt C2M8N3 · UniProt C2M8N4 · UniProt C2M7I7
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