MolNFT v1 · #65588 · protein
Crystal structure of polynucleotide phosphorylase (pnpase) core bound to RNase E and tungstate
3H1C · Polyribonucleotide nucleotidyltransferase: “Crystal structure of polynucleotide phosphorylase (pnpase) core bound to RNase E and tungstate”. X-ray diffraction, 1 ligand (WO4), 20 pockets (best druggability 0.83). MolNFT v1 #65588 on…
- PDB
- 3H1C
- Type
- protein
- Length
- 6,777 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyribonucleotide nucleotidyltransferase; Ribonuclease E
- EC
- 2.7.7.8, 3.1.26.12
- UniProt
- P05055, P21513
- Ligands
- WO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, K, M, O, R, V, X | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 544 | 34% helix, 27% strand | P05055 |
| D, E, F, H, J, L, N, P, S, U, W, Y | Ribonuclease E (EC 3.1.26.12) | protein | 21 | 14% helix, 24% strand | P21513 |
| G, I, T | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 543 | 35% helix, 25% strand | P05055 |
Ligands and binding sites
- WO4 · Tungstate(vi)ion · ion · 21 copies · chains A, B, C, G, I, K, M, O, R, T, V, X
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 | 837 | 0.83 | 0.86 | 103 | WO4 |
| 2 | 924 | 0.83 | 0.85 | 107 | empty |
| 3 | 1192 | 0.83 | 0.84 | 137 | WO4 |
| 4 | 1163 | 0.82 | 0.83 | 123 | empty |
| 5 | 731 | 0.81 | 0.85 | 83 | empty |
Interfaces
52 interfaces between chains.
- M–O · 2025 Ų buried · 35 hydrogen bonds · protein-protein
- I–K · 2024 Ų buried · 29 hydrogen bonds · protein-protein
- M–R · 2002 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2000 Ų buried · 23 hydrogen bonds · protein-protein
- O–R · 1997 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3H1C · Crystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and… · the same entry in another collection · chain K against K, 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 P05055
- Every structure of UniProt P21513
- Elsewhere: RCSB PDB 3H1C · PDBe 3H1C · UniProt P05055 · UniProt P21513
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