MolNFT v1 · #160618 · protein
Rhinovirus C15 complexed with domain I of receptor CDHR3
6PPO · Capsid protein VP1: “Rhinovirus C15 complexed with domain I of receptor CDHR3”. Electron microscopy, 1 ligand (CA), 8 pockets (best druggability 0.63). MolNFT v1 #160618 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PPO
- Type
- protein
- Length
- 882 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP3; Capsid protein VP2; Capsid protein VP4…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- E5D8F2, Q6ZTQ4
- Ligands
- CA
- Pockets
- 8 · best druggability 0.63
Structure
electron microscopy · 5 distinct chains · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 261 | 8% helix, 27% strand | E5D8F2 |
| B | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 235 | 7% helix, 32% strand | E5D8F2 |
| C | Capsid protein VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 253 | 9% helix, 34% strand | E5D8F2 |
| D | Capsid protein VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 25 | 12% helix, 4% strand | E5D8F2 |
| U | Cadherin-related family member 3 | protein | 108 | 0% helix, 42% strand | Q6ZTQ4 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.63 | 0.80 | 56 | empty |
| 2 | 122 | 0.45 | 0.77 | 20 | empty |
| 3 | 158 | 0.44 | 0.75 | 32 | empty |
| 4 | 116 | 0.43 | 0.77 | 29 | empty |
| 5 | 102 | 0.40 | 0.76 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4060 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 2276 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1622 Ų buried · 18 hydrogen bonds · protein-protein
- B–U · 686 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 613 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6PPO · Rhinovirus C15 complexed with domain I of receptor CDHR3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6ZTQ4 · AlphaFold monomer V2.0 prediction for cadherin-related family member 3 (Q6ZTQ4) · a predicted model of the same protein · chain U against A, TM-score 0.94
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 E5D8F2
- Every structure of UniProt Q6ZTQ4
- Elsewhere: RCSB PDB 6PPO · PDBe 6PPO · UniProt E5D8F2 · UniProt Q6ZTQ4
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