MolNFT v1 · #15648 · protein + RNA
Hc-J4 RNA polymerase complexed with short RNA template strand
1NB7 · 5'-R(*UP*UP*UP*U)-3': “Hc-J4 RNA polymerase complexed with short RNA template strand”. X-ray diffraction, 1 ligand (MN), 14 pockets (best druggability 0.83). MolNFT v1 #15648 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1NB7
- Type
- protein + RNA
- Length
- 1,139 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*UP*UP*U)-3'; Polyprotein
- EC
- 2.7.7.48
- UniProt
- Q02828
- Ligands
- MN
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 5'-R(*UP*UP*UP*U)-3' | rna | 4 | — | — |
| A | Polyprotein (EC 2.7.7.48) | protein | 566 | 48% helix, 14% strand | Q02828 |
| B | Polyprotein (EC 2.7.7.48) | protein | 565 | 47% helix, 15% strand | Q02828 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.83 | 0.84 | 75 | MN |
| 2 | 1139 | 0.82 | 0.84 | 81 | MN |
| 3 | 691 | 0.68 | 0.76 | 75 | empty |
| 4 | 135 | 0.51 | 0.80 | 23 | empty |
| 5 | 173 | 0.50 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- E–A · 744 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–B · 712 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 424 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1NB7 · HC-J4 RNA polymerase complexed with short RNA template strand · the same entry in another collection · chain E against E, 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 Q02828
- Elsewhere: RCSB PDB 1NB7 · PDBe 1NB7 · UniProt Q02828
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