MolNFT v1 · #160970 · protein + RNA
Structure of the human respiratory syncytial virus M2-1 protein in complex with a short positive-sense gene-end RNA
6PZQ · Matrix M2-1: “Structure of the human respiratory syncytial virus M2-1 protein in complex with a short positive-sense…”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.78). MolNFT v1 #160970 on GenesisL1: 3D…
- PDB
- 6PZQ
- Type
- protein + RNA
- Length
- 633 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix M2-1; RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3')
- UniProt
- P04545
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix M2-1 | protein | 157 | 60% helix, 1% strand | P04545 |
| B | Matrix M2-1 | protein | 155 | 66% helix, 1% strand | P04545 |
| C | Matrix M2-1 | protein | 152 | 67% helix, 1% strand | P04545 |
| D | Matrix M2-1 | protein | 156 | 69% helix, 1% strand | P04545 |
| I | RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3') | rna | 6 | — | — |
| J | RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3') | rna | 7 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, I, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.78 | 0.87 | 62 | empty |
| 2 | 335 | 0.76 | 0.87 | 42 | empty |
| 3 | 254 | 0.74 | 0.88 | 36 | empty |
| 4 | 345 | 0.71 | 0.83 | 44 | empty |
| 5 | 175 | 0.53 | 0.79 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1660 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1628 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1627 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1588 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 276 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PZQ · Structure of the human respiratory syncytial virus M2-1 protein in complex with a short… · 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 P04545
- Elsewhere: RCSB PDB 6PZQ · PDBe 6PZQ · UniProt P04545
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