Research workbench
Coxsackievirus A24V in complex with the D1-D2 fragment of icam-1
Analyse Coxsackievirus A24V in complex with the D1-D2 fragment of icam-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIT
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; Intercellular adhesion molecule 1
- UniProt
- G3C8J7, A0A088F913, Q0GYP7, P05362
- Pockets
- 6 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | VP1 | protein | 280 | 10% helix, 29% strand | G3C8J7 |
| 2 | VP2 | protein | 264 | 8% helix, 33% strand | A0A088F913 |
| 3 | VP3 | protein | 231 | 6% helix, 29% strand | Q0GYP7 |
| 4 | Intercellular adhesion molecule 1 | protein | 85 | 0% helix, 38% strand | P05362 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.79 | 0.84 | 79 | empty |
| 2 | 266 | 0.64 | 0.82 | 30 | empty |
| 3 | 416 | 0.64 | 0.78 | 48 | empty |
| 4 | 212 | 0.50 | 0.76 | 25 | empty |
| 5 | 70 | 0.32 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- 1–2 · 2378 Ų buried · 41 hydrogen bonds · protein-protein
- 1–3 · 1477 Ų buried · 18 hydrogen bonds · protein-protein
- 2–3 · 795 Ų buried · 12 hydrogen bonds · protein-protein
- 1–4 · 712 Ų buried · 10 hydrogen bonds · protein-protein
- 2–4 · 368 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6EIT · Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P05362 · AlphaFold monomer V2.0 prediction for intercellular adhesion molecule 1 (P05362) · a predicted model of the same protein · chain 4 against A, TM-score 0.92
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 G3C8J7
- Every structure of UniProt A0A088F913
- Every structure of UniProt Q0GYP7
- Every structure of UniProt P05362
- Elsewhere: RCSB PDB 6EIT · PDBe 6EIT · UniProt G3C8J7 · UniProt A0A088F913 · UniProt Q0GYP7 · UniProt P05362
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