MolNFT v1 · #164534 · protein + RNA
Bat influenza a polymerase elongation complex with incoming UTP analogue (complete polymerase)
6T0V · Polymerase acidic protein: “Bat influenza a polymerase elongation complex with incoming UTP analogue (complete polymerase)”. Electron microscopy, 4 ligands (GTG, M4H, 2KH), 20 pockets (best druggability 0.90). MolNFT v1 #164534 on…
- PDB
- 6T0V
- Type
- protein + RNA
- Length
- 2,233 residues
- Chains
- 6
- Method
- electron microscopy
- 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
- GTG, M4H, 2KH, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 6 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 705 | 42% helix, 17% strand | H6QM92 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 745 | 43% helix, 16% strand | H6QM91 |
| C | Polymerase basic protein 2 | protein | 740 | 32% helix, 22% strand | H6QM90 |
| V | 5' vrna | rna | 14 | — | — |
| R | 3' vrna | rna | 18 | — | — |
| M | Capped mRNA | rna | 11 | — | — |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains C, M
- M4H · 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid · ligand · chains A
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · chains B, R, M
- MG · Magnesium ion · metal · 5 copies · chains A, B, M
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 | 862 | 0.90 | 0.93 | 106 | 2KH, MG |
| 2 | 575 | 0.85 | 0.90 | 60 | empty |
| 3 | 474 | 0.84 | 0.92 | 67 | empty |
| 4 | 389 | 0.84 | 0.93 | 71 | empty |
| 5 | 258 | 0.80 | 0.92 | 55 | empty |
Interfaces
13 interfaces between chains.
- A–B · 9061 Ų buried · 137 hydrogen bonds · protein-protein
- B–C · 7523 Ų buried · 82 hydrogen bonds · protein-protein
- B–R · 1819 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–V · 1576 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–C · 1537 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6T0V · Bat Influenza A polymerase elongation complex with incoming UTP analogue (complete… · 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 6T0V · PDBe 6T0V · UniProt H6QM92 · UniProt H6QM91 · UniProt H6QM90
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