MolNFT v1 · #3800 · protein
Cryo-EM structure of human rhinovirus 14 (HRV14) complexed with a two- domain fragment of its cellular receptor, intercellular adhesion molecule-1 (D1D2-icam-1). implications for virus-receptor interactions. alpha carbons only
1D3I · Protein (intercellular adhesion molecule-1): “Cryo-EM structure of human rhinovirus 14 (HRV14) complexed with a two- domain fragment of its cellular…”. Electron microscopy, 1 pocket (best druggability 0.37). MolNFT v1 #3800 on…
- PDB
- 1D3I
- Type
- protein
- Length
- 989 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (intercellular adhesion molecule-1); Protein (rhinovirus 14 coat protein VP1)…
- UniProt
- P05362, P03303
- Pockets
- 1 · best druggability 0.37
Structure
electron microscopy · 5 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Protein (intercellular adhesion molecule-1) | protein | 185 | 0% helix, 0% strand | P05362 |
| 1 | Protein (rhinovirus 14 coat protein VP1) | protein | 273 | 0% helix, 0% strand | P03303 |
| 2 | Protein (rhinovirus 14 coat protein VP2) | protein | 255 | 0% helix, 0% strand | P03303 |
| 3 | Protein (rhinovirus 14 coat protein VP3) | protein | 236 | 0% helix, 0% strand | P03303 |
| 4 | Protein (rhinovirus 14 coat protein VP4) | protein | 40 | 0% helix, 0% strand | P03303 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.37 | 0.72 | 27 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 593 Ų buried · 0 hydrogen bonds · protein-protein
- 1–2 · 457 Ų buried · 0 hydrogen bonds · protein-protein
- 2–3 · 214 Ų buried · 0 hydrogen bonds · protein-protein
- 1–4 · 167 Ų buried · 0 hydrogen bonds · protein-protein
- 3–4 · 127 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1D3I · Cryo-EM structure of human rhinovirus 14 (HRV14) complexed with a two-domain fragment of… · the same entry in another collection · chain 3 against 3, TM-score 1.00
- P05362 · AlphaFold monomer V2.0 prediction for intercellular adhesion molecule 1 (P05362) · a predicted model of the same protein · chain I against A, TM-score 0.98
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 P05362
- Every structure of UniProt P03303
- Elsewhere: RCSB PDB 1D3I · PDBe 1D3I · UniProt P05362 · UniProt P03303
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