MolNFT v1 · #83359 · protein + RNA
TRNA processing enzyme complex 2
3WFR · RNA (74-mer): “TRNA processing enzyme complex 2”. X-ray diffraction, 3 ligands (CTP, POP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #83359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WFR
- Type
- protein + RNA
- Length
- 2,100 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (74-mer); RNA (75-mer); Poly a polymerase
- EC
- 2.7.7.72
- UniProt
- O67911
- Ligands
- CTP, POP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (74-mer) | rna | 74 | — | — |
| C, D | RNA (75-mer) | rna | 75 | — | — |
| E | Poly a polymerase (EC 2.7.7.72) | protein | 439 | 59% helix, 10% strand | O67911 |
| F | Poly a polymerase (EC 2.7.7.72) | protein | 439 | 56% helix, 10% strand | O67911 |
| G | Poly a polymerase (EC 2.7.7.72) | protein | 461 | 58% helix, 10% strand | O67911 |
| H | Poly a polymerase (EC 2.7.7.72) | protein | 463 | 59% helix, 10% strand | O67911 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- MG · Magnesium ion · metal · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.80 | 0.86 | 56 | POP, MG |
| 2 | 831 | 0.79 | 0.82 | 76 | POP |
| 3 | 761 | 0.79 | 0.83 | 77 | POP |
| 4 | 693 | 0.77 | 0.82 | 71 | POP |
| 5 | 810 | 0.77 | 0.81 | 86 | empty |
Interfaces
9 interfaces between chains.
- G–H · 1988 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1949 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 1362 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–G · 1304 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–F · 1079 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
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 O67911
- Elsewhere: RCSB PDB 3WFR · PDBe 3WFR · UniProt O67911
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