MolNFT v1 · #29416 · protein
Cryo-EM structure of human coxsackievirus A21 complexed with five domain icam-1KILIFI
1Z7Z: “Cryo-EM structure of human coxsackievirus A21 complexed with five domain icam-1KILIFI”. Electron microscopy, 1 ligand (NAG), 6 pockets (best druggability 0.83). MolNFT v1 #29416 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1Z7Z
- Type
- protein
- Length
- 1,120 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human coxsackievirus A21; Intercellular adhesion molecule-1
- UniProt
- P05362
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Human coxsackievirus A21 | protein | 214 | 9% helix, 37% strand | — |
| 2 | Human coxsackievirus A21 | protein | 263 | 12% helix, 38% strand | — |
| 3 | Human coxsackievirus A21 | protein | 192 | 9% helix, 35% strand | — |
| 4 | Human coxsackievirus A21 | protein | 12 | 0% helix, 8% strand | — |
| 5 | Human coxsackievirus A21 | protein | 5 | 0% helix, 0% strand | — |
| I | Intercellular adhesion molecule-1 | protein | 434 | 4% helix, 58% strand | P05362 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.83 | 0.92 | 57 | empty |
| 2 | 694 | 0.68 | 0.76 | 71 | empty |
| 3 | 350 | 0.59 | 0.77 | 34 | empty |
| 4 | 215 | 0.52 | 0.76 | 22 | empty |
| 5 | 76 | 0.33 | 0.74 | 17 | empty |
Interfaces
8 interfaces between chains.
- 1–2 · 2130 Ų buried · 43 hydrogen bonds · protein-protein
- 1–3 · 1253 Ų buried · 28 hydrogen bonds · protein-protein
- 3–4 · 854 Ų buried · 15 hydrogen bonds · protein-protein
- 2–3 · 810 Ų buried · 12 hydrogen bonds · protein-protein
- 1–I · 670 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 1Z7Z · Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi · 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 0.88
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
- Elsewhere: RCSB PDB 1Z7Z · PDBe 1Z7Z · UniProt P05362
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