MolNFT v1 · #126454 · protein + RNA
Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated pol II ctd
5M3H · Polymerase acidic protein: “Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated pol II ctd”. X-ray diffraction, 2 ligands (ZN, PO4), 20 pockets (best druggability 0.86). MolNFT v1 #126454 on…
- PDB
- 5M3H
- Type
- protein + RNA
- Length
- 2,223 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
- EC
- 2.7.7.48
- UniProt
- H6QM92, H6QM91, H6QM90
- Ligands
- ZN, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 699 | 42% helix, 17% strand | H6QM92 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 750 | 47% helix, 17% strand | H6QM91 |
| C | Polymerase basic protein 2 | protein | 730 | 38% helix, 23% strand | H6QM90 |
| R | RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3') | rna | 12 | — | — |
| V | RNA 5'-paguaguaacaagaggg | rna | 16 | — | — |
| X | Tyr-ser-pro-thr-sep-pro | protein | 6 | 0% helix, 0% strand | — |
| Y | Tyr-ser-pro-thr-sep-pro | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.86 | 0.87 | 115 | PO4 |
| 2 | 363 | 0.81 | 0.90 | 56 | empty |
| 3 | 785 | 0.79 | 0.82 | 55 | PO4 |
| 4 | 541 | 0.76 | 0.83 | 74 | empty |
| 5 | 202 | 0.74 | 0.90 | 33 | PO4 |
Interfaces
11 interfaces between chains.
- A–B · 9033 Ų buried · 158 hydrogen bonds · protein-protein
- B–C · 7421 Ų buried · 97 hydrogen bonds · protein-protein
- A–C · 1602 Ų buried · 16 hydrogen bonds · protein-protein
- A–V · 1326 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–V · 817 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5M3H · Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated… · the same entry in another collection · chain A against A, 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 H6QM92
- Every structure of UniProt H6QM91
- Every structure of UniProt H6QM90
- Elsewhere: RCSB PDB 5M3H · PDBe 5M3H · UniProt H6QM92 · UniProt H6QM91 · UniProt H6QM90
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